http://genome.sph.umich.edu/w/api.php?action=feedcontributions&feedformat=atom&user=Mreppell 2026-09-30T14:47:38Z User contributions MediaWiki 1.43.1 http://genome.sph.umich.edu/w/index.php?title=Variant_Normalization&diff=7630 2013-07-09T20:14:06Z

<p>Mreppell: /* Parsimony */</p> <hr /> <div>= Introduction =<br /> <br /> Variant representation in Variant Call Format is non-unique. We describe a variant normalization here that is parsimonious and left aligned.<br /> <br /> = Normalization =<br /> <br /> [[Image:left_alignment.png|none|500px|This figure shows multiple representations of a CA tandem repeat. The left shows five possible representations differentiated by color. The right shows the corresponding representation in VCF. The last representation represents the left aligned and parsi- monious representation of the Indel.]] <br /> This figure shows multiple representations of a CA tandem repeat. The left shows five possible representations differentiated by color. The right shows the corresponding representation in VCF. The last representation represents the left aligned and parsimonious representation of the Indel.<br /> <br /> == Parsimony ==<br /> <br /> This refers to the representation of a variant in as few nucleotides as possible. For simple insertions, a representation with more than a single nucleotide from the reference sequence is not considered parsimonious. For simple deletions, a representation of the alternate allele with more than a single reference sequence nucleotide is not considered parsimonious. For the insertion in the figure above, the blue representation is not parsimonious because the second CA can be inferred from the reference sequence. The maroon representation is parsimonious as it contains only a single base from the reference sequence.<br /> <br /> == Left alignment ==<br /> <br /> Left alignment is usually a concept associated with Indels. We define an indel to be left aligned when the variant can not be shifted to the left any further while ensuring that the indel represented is consistent and that no alleles are represented with an empty string (empty allele). The orange representation is not left aligned while the blue representation is.<br /> <br /> === How to observe that a variant is not left aligned or parsimonious on the right side? ===<br /> <br /> If the ends of each allele is the same nucleotide, it is not left aligned or parsimonious on the right side.<br /> <br /> === Proof of left alignment ===<br /> <br /> Suppose an indel is already left aligned. In order to shift the variant to the right, we have to be able to truncate the first leftmost nucleotide in each allele without any loss of information (i.e. we can reconstruct the original alleles from the right aligned version of the variant given the reference genome). In order to guarantee this, the first leftmost nucleotide in each allele should be the same type of nucleotide (in other words, the same as the reference nucleotide).<br /> <br /> The truncation of the first leftmost nucleotide should not result in any empty allele. To achieve this, we need to first extend the rightmost end of each allele by the base observed on the reference sequence and then attempting to truncate the alleles simultaneously on the leftmost end. Thus, an indel is not left aligned if the rightmost nucleotide of each allele is represented by the same type of nucleotide. This procedure also ensures parsimony on the right side of the variants.<br /> <br /> = Algorithm for Normalization =<br /> <br /> The algorithm to normalize a variant; biallelic or multiallelic is as follows:<br /> <br /> [[Image:variant_normalization_algorithm.png|none|500px|Lines 1 to 3 ensures parsimonious representation on the left side. Lines 4 to 9 performs the left alignment and ensures parsimonious representation on the right side. Although we refer to this as a left alignment, this algorithm also ensures a parsimonious representation of Indels. In the case of STRs, we might prefer the repeat units be retained.]]<br /> <br /> Lines 1 to 3 ensures parsimonious representation on the left side. Lines 4 to 9 performs the left alignment and ensures parsimonious representation on the right side. In the case of STRs, we might prefer the repeat units be retained.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=Variant_Normalization&diff=7629 2013-07-09T20:13:48Z

<p>Mreppell: /* Parsimony */</p> <hr /> <div>= Introduction =<br /> <br /> Variant representation in Variant Call Format is non-unique. We describe a variant normalization here that is parsimonious and left aligned.<br /> <br /> = Normalization =<br /> <br /> [[Image:left_alignment.png|none|500px|This figure shows multiple representations of a CA tandem repeat. The left shows five possible representations differentiated by color. The right shows the corresponding representation in VCF. The last representation represents the left aligned and parsi- monious representation of the Indel.]] <br /> This figure shows multiple representations of a CA tandem repeat. The left shows five possible representations differentiated by color. The right shows the corresponding representation in VCF. The last representation represents the left aligned and parsimonious representation of the Indel.<br /> <br /> == Parsimony ==<br /> <br /> This refers to the representation of a variant in as few nucleotides as possible. For insertions, a representation with more than a single nucleotide from the reference sequence is not considered parsimonious. For deletions, a representation of the alternate allele with more than a single reference sequence nucleotide is not considered parsimonious. For the insertion in the figure above, the blue representation is not parsimonious because the second CA can be inferred from the reference sequence. The maroon representation is parsimonious as it contains only a single base from the reference sequence.<br /> <br /> == Left alignment ==<br /> <br /> Left alignment is usually a concept associated with Indels. We define an indel to be left aligned when the variant can not be shifted to the left any further while ensuring that the indel represented is consistent and that no alleles are represented with an empty string (empty allele). The orange representation is not left aligned while the blue representation is.<br /> <br /> === How to observe that a variant is not left aligned or parsimonious on the right side? ===<br /> <br /> If the ends of each allele is the same nucleotide, it is not left aligned or parsimonious on the right side.<br /> <br /> === Proof of left alignment ===<br /> <br /> Suppose an indel is already left aligned. In order to shift the variant to the right, we have to be able to truncate the first leftmost nucleotide in each allele without any loss of information (i.e. we can reconstruct the original alleles from the right aligned version of the variant given the reference genome). In order to guarantee this, the first leftmost nucleotide in each allele should be the same type of nucleotide (in other words, the same as the reference nucleotide).<br /> <br /> The truncation of the first leftmost nucleotide should not result in any empty allele. To achieve this, we need to first extend the rightmost end of each allele by the base observed on the reference sequence and then attempting to truncate the alleles simultaneously on the leftmost end. Thus, an indel is not left aligned if the rightmost nucleotide of each allele is represented by the same type of nucleotide. This procedure also ensures parsimony on the right side of the variants.<br /> <br /> = Algorithm for Normalization =<br /> <br /> The algorithm to normalize a variant; biallelic or multiallelic is as follows:<br /> <br /> [[Image:variant_normalization_algorithm.png|none|500px|Lines 1 to 3 ensures parsimonious representation on the left side. Lines 4 to 9 performs the left alignment and ensures parsimonious representation on the right side. Although we refer to this as a left alignment, this algorithm also ensures a parsimonious representation of Indels. In the case of STRs, we might prefer the repeat units be retained.]]<br /> <br /> Lines 1 to 3 ensures parsimonious representation on the left side. Lines 4 to 9 performs the left alignment and ensures parsimonious representation on the right side. In the case of STRs, we might prefer the repeat units be retained.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=Variant_Normalization&diff=7628 2013-07-09T20:11:49Z

<p>Mreppell: /* Parsimony */</p> <hr /> <div>= Introduction =<br /> <br /> Variant representation in Variant Call Format is non-unique. We describe a variant normalization here that is parsimonious and left aligned.<br /> <br /> = Normalization =<br /> <br /> [[Image:left_alignment.png|none|500px|This figure shows multiple representations of a CA tandem repeat. The left shows five possible representations differentiated by color. The right shows the corresponding representation in VCF. The last representation represents the left aligned and parsi- monious representation of the Indel.]] <br /> This figure shows multiple representations of a CA tandem repeat. The left shows five possible representations differentiated by color. The right shows the corresponding representation in VCF. The last representation represents the left aligned and parsimonious representation of the Indel.<br /> <br /> == Parsimony ==<br /> <br /> This refers to the representation of a variant in as few nucleotides as possible. For insertions, a representation with more than a single nucleotide from the reference sequence is not considered parsimonious. For deletions, a representation of the alternate allele with more than a single reference sequence nucleotide is not considered parsimonious. For the insertion in the figure above, the blue representation is not parsimonious because the second CA can be inferred from the reference sequence. The maroon representation is parsimonious as the alternate allele contains only a single base from the reference sequence.<br /> <br /> == Left alignment ==<br /> <br /> Left alignment is usually a concept associated with Indels. We define an indel to be left aligned when the variant can not be shifted to the left any further while ensuring that the indel represented is consistent and that no alleles are represented with an empty string (empty allele). The orange representation is not left aligned while the blue representation is.<br /> <br /> === How to observe that a variant is not left aligned or parsimonious on the right side? ===<br /> <br /> If the ends of each allele is the same nucleotide, it is not left aligned or parsimonious on the right side.<br /> <br /> === Proof of left alignment ===<br /> <br /> Suppose an indel is already left aligned. In order to shift the variant to the right, we have to be able to truncate the first leftmost nucleotide in each allele without any loss of information (i.e. we can reconstruct the original alleles from the right aligned version of the variant given the reference genome). In order to guarantee this, the first leftmost nucleotide in each allele should be the same type of nucleotide (in other words, the same as the reference nucleotide).<br /> <br /> The truncation of the first leftmost nucleotide should not result in any empty allele. To achieve this, we need to first extend the rightmost end of each allele by the base observed on the reference sequence and then attempting to truncate the alleles simultaneously on the leftmost end. Thus, an indel is not left aligned if the rightmost nucleotide of each allele is represented by the same type of nucleotide. This procedure also ensures parsimony on the right side of the variants.<br /> <br /> = Algorithm for Normalization =<br /> <br /> The algorithm to normalize a variant; biallelic or multiallelic is as follows:<br /> <br /> [[Image:variant_normalization_algorithm.png|none|500px|Lines 1 to 3 ensures parsimonious representation on the left side. Lines 4 to 9 performs the left alignment and ensures parsimonious representation on the right side. Although we refer to this as a left alignment, this algorithm also ensures a parsimonious representation of Indels. In the case of STRs, we might prefer the repeat units be retained.]]<br /> <br /> Lines 1 to 3 ensures parsimonious representation on the left side. Lines 4 to 9 performs the left alignment and ensures parsimonious representation on the right side. In the case of STRs, we might prefer the repeat units be retained.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=Variant_Normalization&diff=7627 2013-07-09T20:10:02Z

<p>Mreppell: /* Parsimony */</p> <hr /> <div>= Introduction =<br /> <br /> Variant representation in Variant Call Format is non-unique. We describe a variant normalization here that is parsimonious and left aligned.<br /> <br /> = Normalization =<br /> <br /> [[Image:left_alignment.png|none|500px|This figure shows multiple representations of a CA tandem repeat. The left shows five possible representations differentiated by color. The right shows the corresponding representation in VCF. The last representation represents the left aligned and parsi- monious representation of the Indel.]] <br /> This figure shows multiple representations of a CA tandem repeat. The left shows five possible representations differentiated by color. The right shows the corresponding representation in VCF. The last representation represents the left aligned and parsimonious representation of the Indel.<br /> <br /> == Parsimony ==<br /> <br /> This refers to the representation of a variant in as few nucleotides as possible. For insertions, a representation with more than a single reference nucleotide is not considered parsimonious. For deletions, a representation with more than a single alternate nucleotide is not considered parsimonious. For the insertion in the figure above, the blue representation is not parsimonious because the second CA can be inferred from the reference sequence. The maroon representation is parsimonious, the alternate allele contains only a single base from the reference sequence.<br /> <br /> == Left alignment ==<br /> <br /> Left alignment is usually a concept associated with Indels. We define an indel to be left aligned when the variant can not be shifted to the left any further while ensuring that the indel represented is consistent and that no alleles are represented with an empty string (empty allele). The orange representation is not left aligned while the blue representation is.<br /> <br /> === How to observe that a variant is not left aligned or parsimonious on the right side? ===<br /> <br /> If the ends of each allele is the same nucleotide, it is not left aligned or parsimonious on the right side.<br /> <br /> === Proof of left alignment ===<br /> <br /> Suppose an indel is already left aligned. In order to shift the variant to the right, we have to be able to truncate the first leftmost nucleotide in each allele without any loss of information (i.e. we can reconstruct the original alleles from the right aligned version of the variant given the reference genome). In order to guarantee this, the first leftmost nucleotide in each allele should be the same type of nucleotide (in other words, the same as the reference nucleotide).<br /> <br /> The truncation of the first leftmost nucleotide should not result in any empty allele. To achieve this, we need to first extend the rightmost end of each allele by the base observed on the reference sequence and then attempting to truncate the alleles simultaneously on the leftmost end. Thus, an indel is not left aligned if the rightmost nucleotide of each allele is represented by the same type of nucleotide. This procedure also ensures parsimony on the right side of the variants.<br /> <br /> = Algorithm for Normalization =<br /> <br /> The algorithm to normalize a variant; biallelic or multiallelic is as follows:<br /> <br /> [[Image:variant_normalization_algorithm.png|none|500px|Lines 1 to 3 ensures parsimonious representation on the left side. Lines 4 to 9 performs the left alignment and ensures parsimonious representation on the right side. Although we refer to this as a left alignment, this algorithm also ensures a parsimonious representation of Indels. In the case of STRs, we might prefer the repeat units be retained.]]<br /> <br /> Lines 1 to 3 ensures parsimonious representation on the left side. Lines 4 to 9 performs the left alignment and ensures parsimonious representation on the right side. In the case of STRs, we might prefer the repeat units be retained.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=Variant_Normalization&diff=7626 2013-07-09T20:05:10Z

<p>Mreppell: /* Parsimony */</p> <hr /> <div>= Introduction =<br /> <br /> Variant representation in Variant Call Format is non-unique. We describe a variant normalization here that is parsimonious and left aligned.<br /> <br /> = Normalization =<br /> <br /> [[Image:left_alignment.png|none|500px|This figure shows multiple representations of a CA tandem repeat. The left shows five possible representations differentiated by color. The right shows the corresponding representation in VCF. The last representation represents the left aligned and parsi- monious representation of the Indel.]] <br /> This figure shows multiple representations of a CA tandem repeat. The left shows five possible representations differentiated by color. The right shows the corresponding representation in VCF. The last representation represents the left aligned and parsimonious representation of the Indel.<br /> <br /> == Parsimony ==<br /> <br /> This refers to the representation of a variant in as few nucleotides as possible. A representation with nucleotides that can be inferred from the reference sequence is not considered parsimonious. The blue variant representation in the figure is not parsimonious because the second CA can be inferred from the reference sequence. The maroon representation is parsimonious, the alternate allele contains only a single base from the reference sequence.<br /> <br /> == Left alignment ==<br /> <br /> Left alignment is usually a concept associated with Indels. We define an indel to be left aligned when the variant can not be shifted to the left any further while ensuring that the indel represented is consistent and that no alleles are represented with an empty string (empty allele). The orange representation is not left aligned while the blue representation is.<br /> <br /> === How to observe that a variant is not left aligned or parsimonious on the right side? ===<br /> <br /> If the ends of each allele is the same nucleotide, it is not left aligned or parsimonious on the right side.<br /> <br /> === Proof of left alignment ===<br /> <br /> Suppose an indel is already left aligned. In order to shift the variant to the right, we have to be able to truncate the first leftmost nucleotide in each allele without any loss of information (i.e. we can reconstruct the original alleles from the right aligned version of the variant given the reference genome). In order to guarantee this, the first leftmost nucleotide in each allele should be the same type of nucleotide (in other words, the same as the reference nucleotide).<br /> <br /> The truncation of the first leftmost nucleotide should not result in any empty allele. To achieve this, we need to first extend the rightmost end of each allele by the base observed on the reference sequence and then attempting to truncate the alleles simultaneously on the leftmost end. Thus, an indel is not left aligned if the rightmost nucleotide of each allele is represented by the same type of nucleotide. This procedure also ensures parsimony on the right side of the variants.<br /> <br /> = Algorithm for Normalization =<br /> <br /> The algorithm to normalize a variant; biallelic or multiallelic is as follows:<br /> <br /> [[Image:variant_normalization_algorithm.png|none|500px|Lines 1 to 3 ensures parsimonious representation on the left side. Lines 4 to 9 performs the left alignment and ensures parsimonious representation on the right side. Although we refer to this as a left alignment, this algorithm also ensures a parsimonious representation of Indels. In the case of STRs, we might prefer the repeat units be retained.]]<br /> <br /> Lines 1 to 3 ensures parsimonious representation on the left side. Lines 4 to 9 performs the left alignment and ensures parsimonious representation on the right side. In the case of STRs, we might prefer the repeat units be retained.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=Variant_Normalization&diff=7625 2013-07-09T20:03:08Z

<p>Mreppell: /* Parsimony */</p> <hr /> <div>= Introduction =<br /> <br /> Variant representation in Variant Call Format is non-unique. We describe a variant normalization here that is parsimonious and left aligned.<br /> <br /> = Normalization =<br /> <br /> [[Image:left_alignment.png|none|500px|This figure shows multiple representations of a CA tandem repeat. The left shows five possible representations differentiated by color. The right shows the corresponding representation in VCF. The last representation represents the left aligned and parsi- monious representation of the Indel.]] <br /> This figure shows multiple representations of a CA tandem repeat. The left shows five possible representations differentiated by color. The right shows the corresponding representation in VCF. The last representation represents the left aligned and parsimonious representation of the Indel.<br /> <br /> == Parsimony ==<br /> <br /> This refers to the representation of a variant in as few nucleotides as possible. A representation with nucleotides that can be inferred from the reference sequence is not considered parsimonious. The blue variant representation in the figure is not parsimonious while the maroon representation is.<br /> <br /> == Left alignment ==<br /> <br /> Left alignment is usually a concept associated with Indels. We define an indel to be left aligned when the variant can not be shifted to the left any further while ensuring that the indel represented is consistent and that no alleles are represented with an empty string (empty allele). The orange representation is not left aligned while the blue representation is.<br /> <br /> === How to observe that a variant is not left aligned or parsimonious on the right side? ===<br /> <br /> If the ends of each allele is the same nucleotide, it is not left aligned or parsimonious on the right side.<br /> <br /> === Proof of left alignment ===<br /> <br /> Suppose an indel is already left aligned. In order to shift the variant to the right, we have to be able to truncate the first leftmost nucleotide in each allele without any loss of information (i.e. we can reconstruct the original alleles from the right aligned version of the variant given the reference genome). In order to guarantee this, the first leftmost nucleotide in each allele should be the same type of nucleotide (in other words, the same as the reference nucleotide).<br /> <br /> The truncation of the first leftmost nucleotide should not result in any empty allele. To achieve this, we need to first extend the rightmost end of each allele by the base observed on the reference sequence and then attempting to truncate the alleles simultaneously on the leftmost end. Thus, an indel is not left aligned if the rightmost nucleotide of each allele is represented by the same type of nucleotide. This procedure also ensures parsimony on the right side of the variants.<br /> <br /> = Algorithm for Normalization =<br /> <br /> The algorithm to normalize a variant; biallelic or multiallelic is as follows:<br /> <br /> [[Image:variant_normalization_algorithm.png|none|500px|Lines 1 to 3 ensures parsimonious representation on the left side. Lines 4 to 9 performs the left alignment and ensures parsimonious representation on the right side. Although we refer to this as a left alignment, this algorithm also ensures a parsimonious representation of Indels. In the case of STRs, we might prefer the repeat units be retained.]]<br /> <br /> Lines 1 to 3 ensures parsimonious representation on the left side. Lines 4 to 9 performs the left alignment and ensures parsimonious representation on the right side. In the case of STRs, we might prefer the repeat units be retained.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=Variant_Normalization&diff=7624 2013-07-09T19:54:07Z

<p>Mreppell: /* Introduction */</p> <hr /> <div>= Introduction =<br /> <br /> Variant representation in Variant Call Format is non-unique. We describe a variant normalization here that is parsimonious and left aligned.<br /> <br /> = Normalization =<br /> <br /> [[Image:left_alignment.png|none|500px|This figure shows multiple representations of a CA tandem repeat. The left shows five possible representations differentiated by color. The right shows the corresponding representation in VCF. The last representation represents the left aligned and parsi- monious representation of the Indel.]] <br /> This figure shows multiple representations of a CA tandem repeat. The left shows five possible representations differentiated by color. The right shows the corresponding representation in VCF. The last representation represents the left aligned and parsimonious representation of the Indel.<br /> <br /> == Parsimony ==<br /> <br /> This refers to the representation of a variant in as few nucleotides as possible. A representation with nucleotides that can be inferred from the reference sequence is not considered parsimonious. The blue variant representation in the figure is non parsimonious while the maroon representation is.<br /> <br /> == Left alignment ==<br /> <br /> Left alignment is usually a concept associated with Indels. We define an indel to be left aligned when the variant can not be shifted to the left any further while ensuring that the indel represented is consistent and that no alleles are represented with an empty string (empty allele). The orange representation is not left aligned while the blue representation is.<br /> <br /> === How to observe that a variant is not left aligned or parsimonious on the right side? ===<br /> <br /> If the ends of each allele is the same nucleotide, it is not left aligned or parsimonious on the right side.<br /> <br /> === Proof of left alignment ===<br /> <br /> Suppose an indel is already left aligned. In order to shift the variant to the right, we have to be able to truncate the first leftmost nucleotide in each allele without any loss of information (i.e. we can reconstruct the original alleles from the right aligned version of the variant given the reference genome). In order to guarantee this, the first leftmost nucleotide in each allele should be the same type of nucleotide (in other words, the same as the reference nucleotide).<br /> <br /> The truncation of the first leftmost nucleotide should not result in any empty allele. To achieve this, we need to first extend the rightmost end of each allele by the base observed on the reference sequence and then attempting to truncate the alleles simultaneously on the leftmost end. Thus, an indel is not left aligned if the rightmost nucleotide of each allele is represented by the same type of nucleotide. This procedure also ensures parsimony on the right side of the variants.<br /> <br /> = Algorithm for Normalization =<br /> <br /> The algorithm to normalize a variant; biallelic or multiallelic is as follows:<br /> <br /> [[Image:variant_normalization_algorithm.png|none|500px|Lines 1 to 3 ensures parsimonious representation on the left side. Lines 4 to 9 performs the left alignment and ensures parsimonious representation on the right side. Although we refer to this as a left alignment, this algorithm also ensures a parsimonious representation of Indels. In the case of STRs, we might prefer the repeat units be retained.]]<br /> <br /> Lines 1 to 3 ensures parsimonious representation on the left side. Lines 4 to 9 performs the left alignment and ensures parsimonious representation on the right side. In the case of STRs, we might prefer the repeat units be retained.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=Variant_Normalization&diff=7623 2013-07-09T19:53:41Z

<p>Mreppell: /* Parsimony */</p> <hr /> <div>= Introduction =<br /> <br /> Variant representation in Variant Call Format is non unique. We describe a variant normalization here that is parsimonious and left aligned.<br /> <br /> = Normalization =<br /> <br /> [[Image:left_alignment.png|none|500px|This figure shows multiple representations of a CA tandem repeat. The left shows five possible representations differentiated by color. The right shows the corresponding representation in VCF. The last representation represents the left aligned and parsi- monious representation of the Indel.]] <br /> This figure shows multiple representations of a CA tandem repeat. The left shows five possible representations differentiated by color. The right shows the corresponding representation in VCF. The last representation represents the left aligned and parsimonious representation of the Indel.<br /> <br /> == Parsimony ==<br /> <br /> This refers to the representation of a variant in as few nucleotides as possible. A representation with nucleotides that can be inferred from the reference sequence is not considered parsimonious. The blue variant representation in the figure is non parsimonious while the maroon representation is.<br /> <br /> == Left alignment ==<br /> <br /> Left alignment is usually a concept associated with Indels. We define an indel to be left aligned when the variant can not be shifted to the left any further while ensuring that the indel represented is consistent and that no alleles are represented with an empty string (empty allele). The orange representation is not left aligned while the blue representation is.<br /> <br /> === How to observe that a variant is not left aligned or parsimonious on the right side? ===<br /> <br /> If the ends of each allele is the same nucleotide, it is not left aligned or parsimonious on the right side.<br /> <br /> === Proof of left alignment ===<br /> <br /> Suppose an indel is already left aligned. In order to shift the variant to the right, we have to be able to truncate the first leftmost nucleotide in each allele without any loss of information (i.e. we can reconstruct the original alleles from the right aligned version of the variant given the reference genome). In order to guarantee this, the first leftmost nucleotide in each allele should be the same type of nucleotide (in other words, the same as the reference nucleotide).<br /> <br /> The truncation of the first leftmost nucleotide should not result in any empty allele. To achieve this, we need to first extend the rightmost end of each allele by the base observed on the reference sequence and then attempting to truncate the alleles simultaneously on the leftmost end. Thus, an indel is not left aligned if the rightmost nucleotide of each allele is represented by the same type of nucleotide. This procedure also ensures parsimony on the right side of the variants.<br /> <br /> = Algorithm for Normalization =<br /> <br /> The algorithm to normalize a variant; biallelic or multiallelic is as follows:<br /> <br /> [[Image:variant_normalization_algorithm.png|none|500px|Lines 1 to 3 ensures parsimonious representation on the left side. Lines 4 to 9 performs the left alignment and ensures parsimonious representation on the right side. Although we refer to this as a left alignment, this algorithm also ensures a parsimonious representation of Indels. In the case of STRs, we might prefer the repeat units be retained.]]<br /> <br /> Lines 1 to 3 ensures parsimonious representation on the left side. Lines 4 to 9 performs the left alignment and ensures parsimonious representation on the right side. In the case of STRs, we might prefer the repeat units be retained.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=Variant_Normalization&diff=7622 2013-07-09T19:53:01Z

<p>Mreppell: /* Parsimony */</p> <hr /> <div>= Introduction =<br /> <br /> Variant representation in Variant Call Format is non unique. We describe a variant normalization here that is parsimonious and left aligned.<br /> <br /> = Normalization =<br /> <br /> [[Image:left_alignment.png|none|500px|This figure shows multiple representations of a CA tandem repeat. The left shows five possible representations differentiated by color. The right shows the corresponding representation in VCF. The last representation represents the left aligned and parsi- monious representation of the Indel.]] <br /> This figure shows multiple representations of a CA tandem repeat. The left shows five possible representations differentiated by color. The right shows the corresponding representation in VCF. The last representation represents the left aligned and parsimonious representation of the Indel.<br /> <br /> == Parsimony ==<br /> <br /> This refers to the representation of a variant in as few nucleotides as possible. A representation with nucleotides that can be inferred from the reference sequence is considered not parsimonious. The blue variant representation in the figure is non parsimonious while the maroon representation is.<br /> <br /> == Left alignment ==<br /> <br /> Left alignment is usually a concept associated with Indels. We define an indel to be left aligned when the variant can not be shifted to the left any further while ensuring that the indel represented is consistent and that no alleles are represented with an empty string (empty allele). The orange representation is not left aligned while the blue representation is.<br /> <br /> === How to observe that a variant is not left aligned or parsimonious on the right side? ===<br /> <br /> If the ends of each allele is the same nucleotide, it is not left aligned or parsimonious on the right side.<br /> <br /> === Proof of left alignment ===<br /> <br /> Suppose an indel is already left aligned. In order to shift the variant to the right, we have to be able to truncate the first leftmost nucleotide in each allele without any loss of information (i.e. we can reconstruct the original alleles from the right aligned version of the variant given the reference genome). In order to guarantee this, the first leftmost nucleotide in each allele should be the same type of nucleotide (in other words, the same as the reference nucleotide).<br /> <br /> The truncation of the first leftmost nucleotide should not result in any empty allele. To achieve this, we need to first extend the rightmost end of each allele by the base observed on the reference sequence and then attempting to truncate the alleles simultaneously on the leftmost end. Thus, an indel is not left aligned if the rightmost nucleotide of each allele is represented by the same type of nucleotide. This procedure also ensures parsimony on the right side of the variants.<br /> <br /> = Algorithm for Normalization =<br /> <br /> The algorithm to normalize a variant; biallelic or multiallelic is as follows:<br /> <br /> [[Image:variant_normalization_algorithm.png|none|500px|Lines 1 to 3 ensures parsimonious representation on the left side. Lines 4 to 9 performs the left alignment and ensures parsimonious representation on the right side. Although we refer to this as a left alignment, this algorithm also ensures a parsimonious representation of Indels. In the case of STRs, we might prefer the repeat units be retained.]]<br /> <br /> Lines 1 to 3 ensures parsimonious representation on the left side. Lines 4 to 9 performs the left alignment and ensures parsimonious representation on the right side. In the case of STRs, we might prefer the repeat units be retained.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=FTEC&diff=4657 2012-02-17T15:21:45Z

<p>Mreppell: </p> <hr /> <div>FTEC is a coalescent simulation program developed by Mark Reppell, Michael Boehnke, and Sebastian Zöllner capable of modeling samples drawn from a population which has undergone faster than exponential growth.<br /> <br /> =Installation and Compilation=<br /> <br /> ==Unix==<br /> <br /> 1) Download the appropriate file below &lt;br&gt;<br /> 2) Place downloaded file in the directory where you would like the program to reside &lt;br&gt;<br /> 3) Unzip the file with the command 'gunzip Filename.tar.gz' and then unzar the file with the command 'tar -xf Filename.tar' &lt;br&gt;<br /> 4) Inside the new directory /FTEC which has been created enter the command 'make' &lt;br&gt;<br /> 5) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'<br /> <br /> ==Windows with MinGW==<br /> 1) Instructions for Installing MinGW and MSYS can be found here: [[Installing MinGW &amp; MSYS on Windows]] &lt;br&gt;<br /> 2) Download the appropriate file from below and place it in the folder /msys/1.0/home/user/ where &quot;user&quot; is your user account name &lt;br&gt;<br /> 3) Open the MSYS command line window &lt;br&gt;<br /> 4) Unzip the file using the command &quot;gunzip File_Name.tar.gz&quot; and then untar the file with the command &quot;tar xf Filename.tar&quot; &lt;br&gt;<br /> 5) Enter the newly created folder /FTEC and enter the command &quot;make&quot; &lt;br&gt;<br /> 6) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'<br /> <br /> <br /> For information on how to use the simulator see the user's guide below.<br /> <br /> = Download =<br /> <br /> FTEC requires header files from both the Boost and TCLAP libraries to compile and run. There are 3 available downloads below, differing in which of these library files they contain, so that a user can select the most appropriate download for their system. If a user's system already includes a library and they download a version of ftec that includes the library's header files the program will compile without problem, so if there is any uncertainty download the larger source file below.<br /> <br /> [[Media:FTEC_withboost.tar.gz‎‎| Program files with both Boost and TCLAP header files (300 Kb) ]] &lt;br&gt;<br /> [[Media:FTEC_noboost.tar.gz | Program files with TCLAP header files (58 Kb)]] &lt;br&gt;<br /> [[Media:FTEC_src_only.tar.gz | Program files without Boost or TCLAP header files (27 Kb)]] &lt;br&gt;<br /> <br /> <br /> More information on [http://www.boost.org/ Boost] and the [http://www.boost.org/doc/libs/1_48_0/doc/html/boost_random.html Boost Random Number Library]&lt;br&gt;<br /> More information on the [http://tclap.sourceforge.net/ TCLAP Library]<br /> <br /> == Documentation ==<br /> <br /> [[Media:Fte_Document_06012012.pdf‎ | User's guide]]</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=File:FTEC_noboost.tar.gz&diff=4613 2012-02-14T21:29:31Z

<p>Mreppell: uploaded a new version of &quot;File:FTEC noboost.tar.gz&quot;</p> <hr /> <div>FTEC Source Code with TCLAP header files but without Boost header files.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=File:FTEC_withboost.tar.gz&diff=4612 2012-02-14T21:29:14Z

<p>Mreppell: uploaded a new version of &quot;File:FTEC withboost.tar.gz&quot;</p> <hr /> <div>FTEC source code with Boost and TCLAP header files.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=File:FTEC_src_only.tar.gz&diff=4611 2012-02-14T21:28:57Z

<p>Mreppell: uploaded a new version of &quot;File:FTEC src only.tar.gz&quot;</p> <hr /> <div>FTEC source code without TCLAP or Boost header files.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=FTEC&diff=4595 2012-02-14T18:16:50Z

<p>Mreppell: </p> <hr /> <div>FTEC is a coalescent simulation program developed by Mark Reppell, Michael Boehnke, and Sebastian Zöllner capable of modeling samples drawn from a population which has undergone faster than exponential growth.<br /> <br /> =Installation and Compilation=<br /> <br /> ==Unix==<br /> <br /> 1) Download the appropriate file below &lt;br&gt;<br /> 2) Place downloaded file in the directory where you would like the program to reside, unzip and untar the file &lt;br&gt;<br /> 3) Inside the new directory /FTEC which has been created enter the command 'make' &lt;br&gt;<br /> 4) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'<br /> <br /> ==Windows with MinGW==<br /> 1) Instructions for Installing MinGW and MSYS can be found here: [[Installing MinGW &amp; MSYS on Windows]] &lt;br&gt;<br /> 2) Download the appropriate file from below and place it in the folder /msys/1.0/home/user/ where &quot;user&quot; is your user account name &lt;br&gt;<br /> 3) Open the MSYS command line window &lt;br&gt;<br /> 4) Unzip the file using the command &quot;gunzip File_Name.tar.gz&quot; and then untar the file with the command &quot;tar xf File_Name.tar&quot; &lt;br&gt;<br /> 5) Enter the newly created folder /FTEC and enter the command &quot;make&quot; &lt;br&gt;<br /> 6) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'<br /> <br /> <br /> For information on how to use the simulator see the user's guide below.<br /> <br /> = Download =<br /> <br /> FTEC requires header files from both the Boost and TCLAP libraries to compile and run. There are 3 available downloads below, differing in which of these library files they contain, so that a user can select the most appropriate download for their system. If a user's system already includes a library and they download a version of ftec that includes the library's header files the program will compile without problem, so if there is any uncertainty download the larger source file below.<br /> <br /> [[Media:FTEC_withboost.tar.gz‎‎| Program files with both Boost and TCLAP header files (300 Kb) ]] &lt;br&gt;<br /> [[Media:FTEC_noboost.tar.gz | Program files with TCLAP header files (58 Kb)]] &lt;br&gt;<br /> [[Media:FTEC_src_only.tar.gz | Program files without Boost or TCLAP header files (27 Kb)]] &lt;br&gt;<br /> <br /> <br /> More information on [http://www.boost.org/ Boost] and the [http://www.boost.org/doc/libs/1_48_0/doc/html/boost_random.html Boost Random Number Library]&lt;br&gt;<br /> More information on the [http://tclap.sourceforge.net/ TCLAP Library]<br /> <br /> == Documentation ==<br /> <br /> [[Media:Fte_Document_06012012.pdf‎ | User's guide]]</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=FTEC&diff=4594 2012-02-14T18:13:12Z

<p>Mreppell: </p> <hr /> <div>FTEC is a coalescent simulation program developed by Mark Reppell, Michael Boehnke, and Sebastian Zöllner capable of modeling samples drawn from a population which has undergone faster than exponential growth.<br /> <br /> =Installation and Compilation=<br /> <br /> ==Unix==<br /> <br /> 1) Download the appropriate .tar file below &lt;br&gt;<br /> 2) Place downloaded file in the directory where you would like the program to reside and untar the file &lt;br&gt;<br /> 3) Inside the new directory /FTEC which has been created enter the command 'make' &lt;br&gt;<br /> 4) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'<br /> <br /> ==Windows with MinGW==<br /> 1) Instructions for Installing MinGW and MSYS can be found here: [[Installing MinGW &amp; MSYS on Windows]] &lt;br&gt;<br /> 2) Download the appropriate .tar file from below and place it in the folder /msys/1.0/home/user/ where &quot;user&quot; is your user account name &lt;br&gt;<br /> 3) Open the MSYS command line window &lt;br&gt;<br /> 4) Untar the file with the command &quot;tar xf File_Name.tar&quot; &lt;br&gt;<br /> 5) Enter the newly created folder /FTEC and enter the command &quot;make&quot; &lt;br&gt;<br /> 6) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'<br /> <br /> <br /> For information on how to use the simulator see the user's guide below.<br /> <br /> = Download =<br /> <br /> FTEC requires header files from both the Boost and TCLAP libraries to compile and run. There are 3 available downloads below, differing in which of these library files they contain, so that a user can select the most appropriate download for their system. If a user's system already includes a library and they download a version of ftec that includes the library's header files the program will compile without problem, so if there is any uncertainty download the larger source file below.<br /> <br /> [[Media:FTEC_withboost.tar.gz‎‎| Program files with both Boost and TCLAP header files (300 Kb) ]] &lt;br&gt;<br /> [[Media:FTEC_noboost.tar.gz | Program files with TCLAP header files (58 Kb)]] &lt;br&gt;<br /> [[Media:FTEC_src_only.tar.gz | Program files without Boost or TCLAP header files (27 Kb)]] &lt;br&gt;<br /> <br /> <br /> More information on [http://www.boost.org/ Boost] and the [http://www.boost.org/doc/libs/1_48_0/doc/html/boost_random.html Boost Random Number Library]&lt;br&gt;<br /> More information on the [http://tclap.sourceforge.net/ TCLAP Library]<br /> <br /> == Documentation ==<br /> <br /> [[Media:Fte_Document_06012012.pdf‎ | User's guide]]</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=FTEC&diff=4593 2012-02-14T18:12:35Z

<p>Mreppell: </p> <hr /> <div>FTEC is a coalescent simulation program developed by Mark Reppell, Michael Boehnke, and Sebastian Zöllner capable of modeling samples drawn from a population which has undergone faster than exponential growth.<br /> <br /> =Installation and Compilation=<br /> <br /> ==Unix==<br /> <br /> 1) Download the appropriate .tar file below &lt;br&gt;<br /> 2) Place downloaded file in the directory where you would like the program to reside and untar the file &lt;br&gt;<br /> 3) Inside the new directory /FTEC which has been created enter the command 'make' &lt;br&gt;<br /> 4) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'<br /> <br /> ==Windows with MinGW==<br /> 1) Instructions for Installing MinGW and MSYS can be found here: [[Installing MinGW &amp; MSYS on Windows]] &lt;br&gt;<br /> 2) Download the appropriate .tar file from below and place it in the folder /msys/1.0/home/user/ where &quot;user&quot; is your user account name &lt;br&gt;<br /> 3) Open the MSYS command line window &lt;br&gt;<br /> 4) Untar the file with the command &quot;tar xf File_Name.tar&quot; &lt;br&gt;<br /> 5) Enter the newly created folder /FTEC and enter the command &quot;make&quot; &lt;br&gt;<br /> 6) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'<br /> <br /> <br /> For information on how to use the simulator see the user's guide below.<br /> <br /> = Download =<br /> <br /> FTEC requires header files from both the Boost and TCLAP libraries to compile and run. There are 3 available downloads below, differing in which of these library files they contain. File size and download time increase with the inclusion of each set of library files, so a user can select the most appropriate download for their system. If a user's system already includes a library and they download a version of ftec that includes the library's header files the program will compile without problem, so if there is any uncertainty download the larger source file below.<br /> <br /> [[Media:FTEC_withboost.tar.gz‎‎| Program files with both Boost and TCLAP header files (300 Kb) ]] &lt;br&gt;<br /> [[Media:FTEC_noboost.tar.gz | Program files with TCLAP header files (58 Kb)]] &lt;br&gt;<br /> [[Media:FTEC_src_only.tar.gz | Program files without Boost or TCLAP header files (27 Kb)]] &lt;br&gt;<br /> <br /> <br /> More information on [http://www.boost.org/ Boost] and the [http://www.boost.org/doc/libs/1_48_0/doc/html/boost_random.html Boost Random Number Library]&lt;br&gt;<br /> More information on the [http://tclap.sourceforge.net/ TCLAP Library]<br /> <br /> == Documentation ==<br /> <br /> [[Media:Fte_Document_06012012.pdf‎ | User's guide]]</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=FTEC&diff=4592 2012-02-14T18:12:09Z

<p>Mreppell: </p> <hr /> <div>FTEC is a coalescent simulation program developed by Mark Reppell, Michael Boehnke, and Sebastian Zöllner capable of modeling samples drawn from a population which has undergone faster than exponential growth.<br /> <br /> =Installation and Compilation=<br /> <br /> ==Unix==<br /> <br /> 1) Download the appropriate .tar file below &lt;br&gt;<br /> 2) Place downloaded file in the directory where you would like the program to reside and untar the file &lt;br&gt;<br /> 3) Inside the new directory /FTEC which has been created enter the command 'make' &lt;br&gt;<br /> 4) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'<br /> <br /> ==Windows with MinGW==<br /> 1) Instructions for Installing MinGW and MSYS can be found here: [[Installing MinGW &amp; MSYS on Windows]] &lt;br&gt;<br /> 2) Download the appropriate .tar file from below and place it in the folder /msys/1.0/home/user/ where &quot;user&quot; is your user account name &lt;br&gt;<br /> 3) Open the MSYS command line window &lt;br&gt;<br /> 4) Untar the file with the command &quot;tar xf File_Name.tar&quot; &lt;br&gt;<br /> 5) Enter the newly created folder /FTEC and enter the command &quot;make&quot; &lt;br&gt;<br /> 6) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'<br /> <br /> <br /> For information on how to use the simulator see the user's guide below.<br /> <br /> = Download =<br /> <br /> FTEC requires header files from both the Boost and TCLAP libraries to compile and run. There are 3 available downloads below, differing in which of these library files they contain. File size and download time increase with the inclusion of each set of library files, so a user can select the most appropriate download for their system. If a user's system already includes a library and they download a version of ftec that includes the library's header files the program will compile without problem, so if there is any uncertainty download the larger source file below.<br /> <br /> [[Media:FTEC_withboost.tar.gz‎‎| Program files with both Boost and TCLAP header files (50 Mb) ]] &lt;br&gt;<br /> [[Media:FTEC_noboost.tar.gz | Program files with TCLAP header files (58 Kb)]] &lt;br&gt;<br /> [[Media:FTEC_src_only.tar.gz | Program files without Boost or TCLAP header files (27 Kb)]] &lt;br&gt;<br /> <br /> <br /> More information on [http://www.boost.org/ Boost] and the [http://www.boost.org/doc/libs/1_48_0/doc/html/boost_random.html Boost Random Number Library]&lt;br&gt;<br /> More information on the [http://tclap.sourceforge.net/ TCLAP Library]<br /> <br /> == Documentation ==<br /> <br /> [[Media:Fte_Document_06012012.pdf‎ | User's guide]]</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=File:FTEC_withboost.tar.gz&diff=4591 2012-02-14T18:11:49Z

<p>Mreppell: FTEC source code with Boost and TCLAP header files.</p> <hr /> <div>FTEC source code with Boost and TCLAP header files.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=FTEC&diff=4590 2012-02-14T18:11:06Z

<p>Mreppell: </p> <hr /> <div>FTEC is a coalescent simulation program developed by Mark Reppell, Michael Boehnke, and Sebastian Zöllner capable of modeling samples drawn from a population which has undergone faster than exponential growth.<br /> <br /> =Installation and Compilation=<br /> <br /> ==Unix==<br /> <br /> 1) Download the appropriate .tar file below &lt;br&gt;<br /> 2) Place downloaded file in the directory where you would like the program to reside and untar the file &lt;br&gt;<br /> 3) Inside the new directory /FTEC which has been created enter the command 'make' &lt;br&gt;<br /> 4) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'<br /> <br /> ==Windows with MinGW==<br /> 1) Instructions for Installing MinGW and MSYS can be found here: [[Installing MinGW &amp; MSYS on Windows]] &lt;br&gt;<br /> 2) Download the appropriate .tar file from below and place it in the folder /msys/1.0/home/user/ where &quot;user&quot; is your user account name &lt;br&gt;<br /> 3) Open the MSYS command line window &lt;br&gt;<br /> 4) Untar the file with the command &quot;tar xf File_Name.tar&quot; &lt;br&gt;<br /> 5) Enter the newly created folder /FTEC and enter the command &quot;make&quot; &lt;br&gt;<br /> 6) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'<br /> <br /> <br /> For information on how to use the simulator see the user's guide below.<br /> <br /> = Download =<br /> <br /> FTEC requires header files from both the Boost and TCLAP libraries to compile and run. There are 3 available downloads below, differing in which of these library files they contain. File size and download time increase with the inclusion of each set of library files, so a user can select the most appropriate download for their system. If a user's system already includes a library and they download a version of ftec that includes the library's header files the program will compile without problem, so if there is any uncertainty download the larger source file below.<br /> <br /> [[Media:FTEC_withboost.tar‎‎| Program files with both Boost and TCLAP header files (50 Mb) ]] &lt;br&gt;<br /> [[Media:FTEC_noboost.tar.gz | Program files with TCLAP header files (58 Kb)]] &lt;br&gt;<br /> [[Media:FTEC_src_only.tar.gz | Program files without Boost or TCLAP header files (27 Kb)]] &lt;br&gt;<br /> <br /> <br /> More information on [http://www.boost.org/ Boost] and the [http://www.boost.org/doc/libs/1_48_0/doc/html/boost_random.html Boost Random Number Library]&lt;br&gt;<br /> More information on the [http://tclap.sourceforge.net/ TCLAP Library]<br /> <br /> == Documentation ==<br /> <br /> [[Media:Fte_Document_06012012.pdf‎ | User's guide]]</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=File:FTEC_noboost.tar.gz&diff=4589 2012-02-14T18:10:32Z

<p>Mreppell: FTEC Source Code with TCLAP header files but without Boost header files.</p> <hr /> <div>FTEC Source Code with TCLAP header files but without Boost header files.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=FTEC&diff=4588 2012-02-14T18:09:45Z

<p>Mreppell: </p> <hr /> <div>FTEC is a coalescent simulation program developed by Mark Reppell, Michael Boehnke, and Sebastian Zöllner capable of modeling samples drawn from a population which has undergone faster than exponential growth.<br /> <br /> =Installation and Compilation=<br /> <br /> ==Unix==<br /> <br /> 1) Download the appropriate .tar file below &lt;br&gt;<br /> 2) Place downloaded file in the directory where you would like the program to reside and untar the file &lt;br&gt;<br /> 3) Inside the new directory /FTEC which has been created enter the command 'make' &lt;br&gt;<br /> 4) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'<br /> <br /> ==Windows with MinGW==<br /> 1) Instructions for Installing MinGW and MSYS can be found here: [[Installing MinGW &amp; MSYS on Windows]] &lt;br&gt;<br /> 2) Download the appropriate .tar file from below and place it in the folder /msys/1.0/home/user/ where &quot;user&quot; is your user account name &lt;br&gt;<br /> 3) Open the MSYS command line window &lt;br&gt;<br /> 4) Untar the file with the command &quot;tar xf File_Name.tar&quot; &lt;br&gt;<br /> 5) Enter the newly created folder /FTEC and enter the command &quot;make&quot; &lt;br&gt;<br /> 6) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'<br /> <br /> <br /> For information on how to use the simulator see the user's guide below.<br /> <br /> = Download =<br /> <br /> FTEC requires header files from both the Boost and TCLAP libraries to compile and run. There are 3 available downloads below, differing in which of these library files they contain. File size and download time increase with the inclusion of each set of library files, so a user can select the most appropriate download for their system. If a user's system already includes a library and they download a version of ftec that includes the library's header files the program will compile without problem, so if there is any uncertainty download the larger source file below.<br /> <br /> [[Media:FTEC_withboost.tar‎‎| Program files with both Boost and TCLAP header files (50 Mb) ]] &lt;br&gt;<br /> [[Media:FTEC_noboost.tar‎ | Program files with TCLAP header files (310 Kb)]] &lt;br&gt;<br /> [[Media:FTEC_src_only.tar.gz | Program files without Boost or TCLAP header files (27 Kb)]] &lt;br&gt;<br /> <br /> <br /> More information on [http://www.boost.org/ Boost] and the [http://www.boost.org/doc/libs/1_48_0/doc/html/boost_random.html Boost Random Number Library]&lt;br&gt;<br /> More information on the [http://tclap.sourceforge.net/ TCLAP Library]<br /> <br /> == Documentation ==<br /> <br /> [[Media:Fte_Document_06012012.pdf‎ | User's guide]]</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=FTEC&diff=4587 2012-02-14T18:09:28Z

<p>Mreppell: </p> <hr /> <div>FTEC is a coalescent simulation program developed by Mark Reppell, Michael Boehnke, and Sebastian Zöllner capable of modeling samples drawn from a population which has undergone faster than exponential growth.<br /> <br /> =Installation and Compilation=<br /> <br /> ==Unix==<br /> <br /> 1) Download the appropriate .tar file below &lt;br&gt;<br /> 2) Place downloaded file in the directory where you would like the program to reside and untar the file &lt;br&gt;<br /> 3) Inside the new directory /FTEC which has been created enter the command 'make' &lt;br&gt;<br /> 4) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'<br /> <br /> ==Windows with MinGW==<br /> 1) Instructions for Installing MinGW and MSYS can be found here: [[Installing MinGW &amp; MSYS on Windows]] &lt;br&gt;<br /> 2) Download the appropriate .tar file from below and place it in the folder /msys/1.0/home/user/ where &quot;user&quot; is your user account name &lt;br&gt;<br /> 3) Open the MSYS command line window &lt;br&gt;<br /> 4) Untar the file with the command &quot;tar xf File_Name.tar&quot; &lt;br&gt;<br /> 5) Enter the newly created folder /FTEC and enter the command &quot;make&quot; &lt;br&gt;<br /> 6) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'<br /> <br /> <br /> For information on how to use the simulator see the user's guide below.<br /> <br /> = Download =<br /> <br /> FTEC requires header files from both the Boost and TCLAP libraries to compile and run. There are 3 available downloads below, differing in which of these library files they contain. File size and download time increase with the inclusion of each set of library files, so a user can select the most appropriate download for their system. If a user's system already includes a library and they download a version of ftec that includes the library's header files the program will compile without problem, so if there is any uncertainty download the larger source file below.<br /> <br /> [[Media:FTEC_withboost.tar‎‎| Program files with both Boost and TCLAP header files (50 Mb) ]] &lt;br&gt;<br /> [[Media:FTEC_noboost.tar‎ | Program files with TCLAP header files (310 Kb)]] &lt;br&gt;<br /> [[Media:FTEC_src_only.tar.gz | Program files without Boost or TCLAP header files (120 Kb)]] &lt;br&gt;<br /> <br /> <br /> More information on [http://www.boost.org/ Boost] and the [http://www.boost.org/doc/libs/1_48_0/doc/html/boost_random.html Boost Random Number Library]&lt;br&gt;<br /> More information on the [http://tclap.sourceforge.net/ TCLAP Library]<br /> <br /> == Documentation ==<br /> <br /> [[Media:Fte_Document_06012012.pdf‎ | User's guide]]</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=File:FTEC_src_only.tar.gz&diff=4586 2012-02-14T18:08:51Z

<p>Mreppell: FTEC source code without TCLAP or Boost header files.</p> <hr /> <div>FTEC source code without TCLAP or Boost header files.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=File:Fte_Document_06012012.pdf&diff=4572 2012-02-14T15:51:55Z

<p>Mreppell: uploaded a new version of &quot;File:Fte Document 06012012.pdf&quot;</p> <hr /> <div>This is the user's guide for the fte coalescent simulation program</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=File:Fte_Document_06012012.pdf&diff=4571 2012-02-14T15:49:38Z

<p>Mreppell: uploaded a new version of &quot;File:Fte Document 06012012.pdf&quot;</p> <hr /> <div>This is the user's guide for the fte coalescent simulation program</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=File:Fte_Document_06012012.pdf&diff=4570 2012-02-14T15:43:23Z

<p>Mreppell: uploaded a new version of &quot;File:Fte Document 06012012.pdf&quot;</p> <hr /> <div>This is the user's guide for the fte coalescent simulation program</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=File:FTEC_withboost.tar&diff=4334 2012-01-23T17:49:25Z

<p>Mreppell: uploaded a new version of &quot;File:FTEC withboost.tar&quot;</p> <hr /> <div>FTEC source code with Boost and TCLAP header files.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=File:FTEC_src_only.tar&diff=4333 2012-01-23T17:49:07Z

<p>Mreppell: uploaded a new version of &quot;File:FTEC src only.tar&quot;</p> <hr /> <div>FTEC source code without TCLAP or Boost header files.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=File:FTEC_noboost.tar&diff=4332 2012-01-23T17:48:51Z

<p>Mreppell: uploaded a new version of &quot;File:FTEC noboost.tar&quot;</p> <hr /> <div>FTEC Source Code with TCLAP header files but without Boost header files.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=File:FTEC_noboost.tar&diff=4330 2012-01-23T15:23:56Z

<p>Mreppell: uploaded a new version of &quot;File:FTEC noboost.tar&quot;</p> <hr /> <div>FTEC Source Code with TCLAP header files but without Boost header files.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=File:FTEC_src_only.tar&diff=4329 2012-01-23T15:23:42Z

<p>Mreppell: uploaded a new version of &quot;File:FTEC src only.tar&quot;</p> <hr /> <div>FTEC source code without TCLAP or Boost header files.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=File:FTEC_withboost.tar&diff=4328 2012-01-23T15:23:20Z

<p>Mreppell: uploaded a new version of &quot;File:FTEC withboost.tar&quot;</p> <hr /> <div>FTEC source code with Boost and TCLAP header files.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=FTEC&diff=4286 2012-01-18T16:03:36Z

<p>Mreppell: </p> <hr /> <div>FTEC is a coalescent simulation program developed by Mark Reppell, Michael Boehnke, and Sebastian Zöllner capable of modeling samples drawn from a population which has undergone faster than exponential growth.<br /> <br /> =Installation and Compilation=<br /> <br /> ==Unix==<br /> <br /> 1) Download the appropriate .tar file below &lt;br&gt;<br /> 2) Place downloaded file in the directory where you would like the program to reside and untar the file &lt;br&gt;<br /> 3) Inside the new directory /FTEC which has been created enter the command 'make' &lt;br&gt;<br /> 4) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'<br /> <br /> ==Windows with MinGW==<br /> 1) Instructions for Installing MinGW and MSYS can be found here: [[Using VirtualBox]] &lt;br&gt;<br /> 2) Download the appropriate .tar file from below and place it in the folder /msys/1.0/home/user/ where &quot;user&quot; is your user account name &lt;br&gt;<br /> 3) Open the MSYS command line window &lt;br&gt;<br /> 4) Untar the file with the command &quot;tar xf File_Name.tar&quot; &lt;br&gt;<br /> 5) Enter the newly created folder /FTEC and enter the command &quot;make&quot; &lt;br&gt;<br /> 6) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'<br /> <br /> <br /> For information on how to use the simulator see the user's guide below.<br /> <br /> = Download =<br /> <br /> FTEC requires header files from both the Boost and TCLAP libraries to compile and run. There are 3 available downloads below, differing in which of these library files they contain. File size and download time increase with the inclusion of each set of library files, so a user can select the most appropriate download for their system. If a user's system already includes a library and they download a version of ftec that includes the library's header files the program will compile without problem, so if there is any uncertainty download the larger source file below.<br /> <br /> [[Media:FTEC_withboost.tar‎‎| Program files with both Boost and TCLAP header files (50 Mb) ]] &lt;br&gt;<br /> [[Media:FTEC_noboost.tar‎ | Program files with TCLAP header files (310 Kb)]] &lt;br&gt;<br /> [[Media:FTEC_src_only.tar‎ | Program files without Boost or TCLAP header files (120 Kb)]] &lt;br&gt;<br /> <br /> <br /> More information on [http://www.boost.org/ Boost] and the [http://www.boost.org/doc/libs/1_48_0/doc/html/boost_random.html Boost Random Number Library]&lt;br&gt;<br /> More information on the [http://tclap.sourceforge.net/ TCLAP Library]<br /> <br /> == Documentation ==<br /> <br /> [[Media:Fte_Document_06012012.pdf‎ | User's guide]]</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=FTEC&diff=4285 2012-01-18T16:00:54Z

<p>Mreppell: </p> <hr /> <div>FTEC is a coalescent simulation program developed by Mark Reppell, Michael Boehnke, and Sebastian Zöllner capable of modeling samples drawn from a population which has undergone faster than exponential growth.<br /> <br /> =Installation and Compilation=<br /> <br /> ==Unix==<br /> <br /> 1) Download the appropriate .tar file below &lt;br&gt;<br /> 2) Place downloaded file in the directory where you would like the program to reside and untar the file &lt;br&gt;<br /> 3) Inside the new directory /FTEC which has been created enter the command 'make' &lt;br&gt;<br /> 4) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'.<br /> <br /> For information on how to use the simulator see the user's guide below.<br /> <br /> ==Windows with MinGW==<br /> 1) Instructions for Installing MinGW and MSYS can be found here: [[Using VirtualBox]] &lt;br&gt;<br /> 2) Download the appropriate .tar file from below and place it in the folder \msys\1.0\home\user\ where &quot;user&quot; is your user account name<br /> 3) Open the MSYS command line window<br /> 4) Untar the file with the command &quot;tar xf File_Name.tar&quot;<br /> 5) Enter the command &quot;make&quot;<br /> 6) <br /> <br /> <br /> == Download ==<br /> <br /> FTEC requires header files from both the Boost and TCLAP libraries to compile and run. There are 3 available downloads below, differing in which of these library files they contain. File size and download time increase with the inclusion of each set of library files, so a user can select the most appropriate download for their system. If a user's system already includes a library and they download a version of ftec that includes the library's header files the program will compile without problem, so if there is any uncertainty download the larger source file below.<br /> <br /> [[Media:FTEC_withboost.tar‎‎| Program files with both Boost and TCLAP header files (50 Mb) ]] &lt;br&gt;<br /> [[Media:FTEC_noboost.tar‎ | Program files with TCLAP header files (310 Kb)]] &lt;br&gt;<br /> [[Media:FTEC_src_only.tar‎ | Program files without Boost or TCLAP header files (120 Kb)]] &lt;br&gt;<br /> <br /> <br /> More information on [http://www.boost.org/ Boost] and the [http://www.boost.org/doc/libs/1_48_0/doc/html/boost_random.html Boost Random Number Library]&lt;br&gt;<br /> More information on the [http://tclap.sourceforge.net/ TCLAP Library]<br /> <br /> == Documentation ==<br /> <br /> [[Media:Fte_Document_06012012.pdf‎ | User's guide]]</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=FTEC&diff=4284 2012-01-18T15:54:01Z

<p>Mreppell: </p> <hr /> <div>FTEC is a coalescent simulation program developed by Mark Reppell, Michael Boehnke, and Sebastian Zöllner capable of modeling samples drawn from a population which has undergone faster than exponential growth.<br /> <br /> ==Unix Installation and Compilation==<br /> <br /> 1) Download the appropriate .tar file below &lt;br&gt;<br /> 2) Place downloaded file in the directory where you would like the program to reside and untar the file &lt;br&gt;<br /> 3) Inside the new directory /FTEC which has been created enter the command 'make' &lt;br&gt;<br /> 4) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'.<br /> <br /> For information on how to use the simulator see the user's guide below.<br /> <br /> ==Windows with MinGW Installation and Compilation==<br /> 1) Instructions for Installing MinGW and MSYS can be found here: [[Using VirtualBox]] &lt;br&gt;<br /> 2) <br /> <br /> <br /> == Download ==<br /> <br /> FTEC requires header files from both the Boost and TCLAP libraries to compile and run. There are 3 available downloads below, differing in which of these library files they contain. File size and download time increase with the inclusion of each set of library files, so a user can select the most appropriate download for their system. If a user's system already includes a library and they download a version of ftec that includes the library's header files the program will compile without problem, so if there is any uncertainty download the larger source file below.<br /> <br /> [[Media:FTEC_withboost.tar‎‎| Program files with both Boost and TCLAP header files (50 Mb) ]] &lt;br&gt;<br /> [[Media:FTEC_noboost.tar‎ | Program files with TCLAP header files (310 Kb)]] &lt;br&gt;<br /> [[Media:FTEC_src_only.tar‎ | Program files without Boost or TCLAP header files (120 Kb)]] &lt;br&gt;<br /> <br /> <br /> More information on [http://www.boost.org/ Boost] and the [http://www.boost.org/doc/libs/1_48_0/doc/html/boost_random.html Boost Random Number Library]&lt;br&gt;<br /> More information on the [http://tclap.sourceforge.net/ TCLAP Library]<br /> <br /> == Documentation ==<br /> <br /> [[Media:Fte_Document_06012012.pdf‎ | User's guide]]</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=FTEC&diff=4282 2012-01-18T15:48:56Z

<p>Mreppell: </p> <hr /> <div>FTEC is a coalescent simulation program developed by Mark Reppell, Michael Boehnke, and Sebastian Zöllner capable of modeling samples drawn from a population which has undergone faster than exponential growth.<br /> <br /> ==Unix Installation and Compilation==<br /> <br /> 1) Download the appropriate .tar file below &lt;br&gt;<br /> 2) Place downloaded file in the directory where you would like the program to reside and untar the file &lt;br&gt;<br /> 3) Inside the new directory /FTEC which has been created enter the command 'make' &lt;br&gt;<br /> 4) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'.<br /> <br /> For information on how to use the simulator see the user's guide below.<br /> <br /> ==Windows with MinGW Installation and Compilation==<br /> 1) If you do not have <br /> <br /> <br /> == Download ==<br /> <br /> FTEC requires header files from both the Boost and TCLAP libraries to compile and run. There are 3 available downloads below, differing in which of these library files they contain. File size and download time increase with the inclusion of each set of library files, so a user can select the most appropriate download for their system. If a user's system already includes a library and they download a version of ftec that includes the library's header files the program will compile without problem, so if there is any uncertainty download the larger source file below.<br /> <br /> [[Media:FTEC_withboost.tar‎‎| Program files with both Boost and TCLAP header files (50 Mb) ]] &lt;br&gt;<br /> [[Media:FTEC_noboost.tar‎ | Program files with TCLAP header files (310 Kb)]] &lt;br&gt;<br /> [[Media:FTEC_src_only.tar‎ | Program files without Boost or TCLAP header files (120 Kb)]] &lt;br&gt;<br /> <br /> <br /> More information on [http://www.boost.org/ Boost] and the [http://www.boost.org/doc/libs/1_48_0/doc/html/boost_random.html Boost Random Number Library]&lt;br&gt;<br /> More information on the [http://tclap.sourceforge.net/ TCLAP Library]<br /> <br /> == Documentation ==<br /> <br /> [[Media:Fte_Document_06012012.pdf‎ | User's guide]]</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=FTEC&diff=4211 2012-01-13T20:15:33Z

<p>Mreppell: </p> <hr /> <div>FTEC is a coalescent simulation program developed by Mark Reppell, Michael Boehnke, and Sebastian Zöllner capable of modeling samples drawn from a population which has undergone faster than exponential growth.<br /> <br /> ==Unix Installation and Compilation==<br /> <br /> 1) Download the appropriate .tar file below &lt;br&gt;<br /> 2) Place downloaded file in the directory where you would like the program to reside and untar the file &lt;br&gt;<br /> 3) Inside the new directory /FTEC which has been created enter the command 'make' &lt;br&gt;<br /> 4) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'.<br /> <br /> For information on how to use the simulator see the user's guide below.<br /> <br /> == Download ==<br /> <br /> FTEC requires header files from both the Boost and TCLAP libraries to compile and run. There are 3 available downloads below, differing in which of these library files they contain. File size and download time increase with the inclusion of each set of library files, so a user can select the most appropriate download for their system. If a user's system already includes a library and they download a version of ftec that includes the library's header files the program will compile without problem, so if there is any uncertainty download the larger source file below.<br /> <br /> [[Media:FTEC_withboost.tar‎‎| Program files with both Boost and TCLAP header files (50 Mb) ]] &lt;br&gt;<br /> [[Media:FTEC_noboost.tar‎ | Program files with TCLAP header files (310 Kb)]] &lt;br&gt;<br /> [[Media:FTEC_src_only.tar‎ | Program files without Boost or TCLAP header files (120 Kb)]] &lt;br&gt;<br /> <br /> <br /> More information on [http://www.boost.org/ Boost] and the [http://www.boost.org/doc/libs/1_48_0/doc/html/boost_random.html Boost Random Number Library]&lt;br&gt;<br /> More information on the [http://tclap.sourceforge.net/ TCLAP Library]<br /> <br /> == Documentation ==<br /> <br /> [[Media:Fte_Document_06012012.pdf‎ | User's guide]]</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=FTEC&diff=4210 2012-01-13T20:15:05Z

<p>Mreppell: </p> <hr /> <div>FTEC is a coalescent simulation program developed by Mark Reppell, Michael Boehnke, and Sebastian Zöllner capable of modeling samples drawn from a population which has undergone faster than exponential growth.<br /> <br /> ==Unix Installation and Compilation==<br /> <br /> 1) Download the appropriate .tar file below &lt;br&gt;<br /> 2) Place downloaded file in the directory where you would like the program to reside and untar the file &lt;br&gt;<br /> 3) Inside the new directory /FTEC which has been created enter the command 'make' &lt;br&gt;<br /> 4) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'.<br /> <br /> For information on how to use the simulator see the user's guide below.<br /> <br /> == Download ==<br /> <br /> FTEC requires header files from both the Boost and TCLAP libraries to compile and run. There are 3 available downloads below, differing in which of these library files they contain. File size and download time increase with the inclusion of each set of library files, so a user can select the most appropriate download for their system. If a user's system already includes a library and they download a version of ftec that includes the library's header files the program will compile without problem, so if there is any uncertainty download the larger source file below.<br /> <br /> [[Media:FTEC_withboost.tar‎‎| Program files with both Boost and TCLAP header files (50 Mb) ]] &lt;br&gt;<br /> [[Media:FTEC_noboost.tar‎ | Program files with TCLAP header files (270 Kb)]] &lt;br&gt;<br /> [[Media:FTEC_src_only.tar‎ | Program files without Boost or TCLAP header files (80 Kb)]] &lt;br&gt;<br /> <br /> <br /> More information on [http://www.boost.org/ Boost] and the [http://www.boost.org/doc/libs/1_48_0/doc/html/boost_random.html Boost Random Number Library]&lt;br&gt;<br /> More information on the [http://tclap.sourceforge.net/ TCLAP Library]<br /> <br /> == Documentation ==<br /> <br /> [[Media:Fte_Document_06012012.pdf‎ | User's guide]]</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=File:FTEC_withboost.tar&diff=4209 2012-01-13T20:11:10Z

<p>Mreppell: FTEC source code with Boost and TCLAP header files.</p> <hr /> <div>FTEC source code with Boost and TCLAP header files.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=File:FTEC_src_only.tar&diff=4208 2012-01-13T20:10:26Z

<p>Mreppell: FTEC source code without TCLAP or Boost header files.</p> <hr /> <div>FTEC source code without TCLAP or Boost header files.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=File:FTEC_noboost.tar&diff=4207 2012-01-13T20:09:51Z

<p>Mreppell: FTEC Source Code with TCLAP header files but without Boost header files.</p> <hr /> <div>FTEC Source Code with TCLAP header files but without Boost header files.</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=File:Fte_Document_06012012.pdf&diff=4203 2012-01-13T15:07:10Z

<p>Mreppell: uploaded a new version of &quot;File:Fte Document 06012012.pdf&quot;</p> <hr /> <div>This is the user's guide for the fte coalescent simulation program</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=FTEC&diff=4202 2012-01-12T21:45:56Z

<p>Mreppell: </p> <hr /> <div>FTEC is a coalescent simulation program developed by Mark Reppell, Michael Boehnke, and Sebastian Zöllner capable of modeling samples drawn from a population which has undergone faster than exponential growth.<br /> <br /> ==Unix Installation and Compilation==<br /> <br /> 1) Download the appropriate .tar file below &lt;br&gt;<br /> 2) Place downloaded file in the directory where you would like the program to reside and untar the file &lt;br&gt;<br /> 3) Inside the new directory /FTEC which has been created enter the command 'make' &lt;br&gt;<br /> 4) An executable file named 'FTEC' should now reside in this directory, this is the simulator and can be run using './FTEC -parameters'.<br /> <br /> For information on how to use the simulator see the user's guide below.<br /> <br /> == Download ==<br /> <br /> FTEC requires header files from both the Boost and TCLAP libraries to compile and run. There are 3 available downloads below, differing in which of these library files they contain. File size and download time increase with the inclusion of each set of library files, so a user can select the most appropriate download for their system. If a user's system already includes a library and they download a version of ftec that includes the library's header files the program will compile without problem, so if there is any uncertainty download the larger source file below.<br /> <br /> [[Media:Fte_v1.36.tar‎| Program files with both Boost and TCLAP header files (50 Mb) ]] &lt;br&gt;<br /> [[Media:Fte_v1.36_noboost.tar | Program files with TCLAP header files (270 Kb)]] &lt;br&gt;<br /> [[Media:Fte_v1.36_src_only.tar | Program files without Boost or TCLAP header files (80 Kb)]] &lt;br&gt;<br /> <br /> <br /> More information on [http://www.boost.org/ Boost] and the [http://www.boost.org/doc/libs/1_48_0/doc/html/boost_random.html Boost Random Number Library]&lt;br&gt;<br /> More information on the [http://tclap.sourceforge.net/ TCLAP Library]<br /> <br /> == Documentation ==<br /> <br /> [[Media:Fte_Document_06012012.pdf‎ | User's guide]]</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=Ftec&diff=4201 2012-01-12T21:45:04Z

<p>Mreppell: moved Ftec to FTEC:&amp;#32;Program has been given a name.</p> <hr /> <div>#REDIRECT [[FTEC]]</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=FTEC&diff=4200 2012-01-12T21:45:04Z

<p>Mreppell: moved Ftec to FTEC:&amp;#32;Program has been given a name.</p> <hr /> <div>ftec is a coalescent simulation program developed by Mark Reppell, Michael Boehnke, and Sebastian Zöllner capable of modeling samples drawn from a population which has undergone faster than exponential growth.<br /> <br /> ==Installation and Compilation==<br /> <br /> 1) Download the appropriate .tar file below &lt;br&gt;<br /> 2) Place downloaded file in the directory where you would like the program to reside and untar the file &lt;br&gt;<br /> 3) Inside the new directory /ftec which has been created enter the command 'make' &lt;br&gt;<br /> 4) An executable file named 'ftec' should now reside in this directory, this is the simulator and can be run using './ftec -parameters'.<br /> <br /> For information on how to use the simulator see the user's guide below.<br /> <br /> == Download ==<br /> <br /> ftec requires header files from both the Boost and TCLAP libraries to compile and run. There are 3 available downloads below, differing in which of these library files they contain. File size and download time increase with the inclusion of each set of library files, so a user can select the most appropriate download for their system. If a user's system already includes a library and they download a version of ftec that includes the library's header files the program will compile without problem, so if there is any uncertainty download the larger source file below.<br /> <br /> [[Media:Fte_v1.36.tar‎| Program files with both Boost and TCLAP header files (50 Mb) ]] &lt;br&gt;<br /> [[Media:Fte_v1.36_noboost.tar | Program files with TCLAP header files (270 Kb)]] &lt;br&gt;<br /> [[Media:Fte_v1.36_src_only.tar | Program files without Boost or TCLAP header files (80 Kb)]] &lt;br&gt;<br /> <br /> <br /> More information on [http://www.boost.org/ Boost] and the [http://www.boost.org/doc/libs/1_48_0/doc/html/boost_random.html Boost Random Number Library]&lt;br&gt;<br /> More information on the [http://tclap.sourceforge.net/ TCLAP Library]<br /> <br /> == Documentation ==<br /> <br /> [[Media:Fte_Document_06012012.pdf‎ | User's guide]]</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=FTEC&diff=4199 2012-01-12T21:32:31Z

<p>Mreppell: </p> <hr /> <div>ftec is a coalescent simulation program developed by Mark Reppell, Michael Boehnke, and Sebastian Zöllner capable of modeling samples drawn from a population which has undergone faster than exponential growth.<br /> <br /> ==Installation and Compilation==<br /> <br /> 1) Download the appropriate .tar file below &lt;br&gt;<br /> 2) Place downloaded file in the directory where you would like the program to reside and untar the file &lt;br&gt;<br /> 3) Inside the new directory /ftec which has been created enter the command 'make' &lt;br&gt;<br /> 4) An executable file named 'ftec' should now reside in this directory, this is the simulator and can be run using './ftec -parameters'.<br /> <br /> For information on how to use the simulator see the user's guide below.<br /> <br /> == Download ==<br /> <br /> ftec requires header files from both the Boost and TCLAP libraries to compile and run. There are 3 available downloads below, differing in which of these library files they contain. File size and download time increase with the inclusion of each set of library files, so a user can select the most appropriate download for their system. If a user's system already includes a library and they download a version of ftec that includes the library's header files the program will compile without problem, so if there is any uncertainty download the larger source file below.<br /> <br /> [[Media:Fte_v1.36.tar‎| Program files with both Boost and TCLAP header files (50 Mb) ]] &lt;br&gt;<br /> [[Media:Fte_v1.36_noboost.tar | Program files with TCLAP header files (270 Kb)]] &lt;br&gt;<br /> [[Media:Fte_v1.36_src_only.tar | Program files without Boost or TCLAP header files (80 Kb)]] &lt;br&gt;<br /> <br /> <br /> More information on [http://www.boost.org/ Boost] and the [http://www.boost.org/doc/libs/1_48_0/doc/html/boost_random.html Boost Random Number Library]&lt;br&gt;<br /> More information on the [http://tclap.sourceforge.net/ TCLAP Library]<br /> <br /> == Documentation ==<br /> <br /> [[Media:Fte_Document_06012012.pdf‎ | User's guide]]</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=Fte&diff=4198 2012-01-12T21:30:40Z

<p>Mreppell: moved Fte to Ftec</p> <hr /> <div>#REDIRECT [[Ftec]]</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=FTEC&diff=4197 2012-01-12T21:30:40Z

<p>Mreppell: moved Fte to Ftec</p> <hr /> <div>fte is a coalescent simulation program developed by Mark Reppell, Michael Boehnke, and Sebastian Zöllner capable of modeling samples drawn from a population which has undergone faster than exponential growth.<br /> <br /> ==Installation and Compilation==<br /> <br /> 1) Download the appropriate .tar file below &lt;br&gt;<br /> 2) Place downloaded file in the directory where you would like the program to reside and untar the file &lt;br&gt;<br /> 3) Inside the new directory /fte which has been created enter the command 'make' &lt;br&gt;<br /> 4) An executable file named 'fte' should now reside in this directory, this is the simulator and can be run using './fte -parameters'.<br /> <br /> For information on how to use the simulator see the user's guide below.<br /> <br /> == Download ==<br /> <br /> fte requires header files from both the Boost and TCLAP libraries to compile and run. There are 3 available downloads below, differing in which of these library files they contain. File size and download time increase with the inclusion of each set of library files, so a user can select the most appropriate download for their system. If a user's system already includes a library and they download a version of fte that includes the library's header files the program will compile without problem, so if there is any uncertainty download the larger source file below.<br /> <br /> [[Media:Fte_v1.36.tar‎| Program files with both Boost and TCLAP header files (50 Mb) ]] &lt;br&gt;<br /> [[Media:Fte_v1.36_noboost.tar | Program files with TCLAP header files (270 Kb)]] &lt;br&gt;<br /> [[Media:Fte_v1.36_src_only.tar | Program files without Boost or TCLAP header files (80 Kb)]] &lt;br&gt;<br /> <br /> <br /> More information on [http://www.boost.org/ Boost] and the [http://www.boost.org/doc/libs/1_48_0/doc/html/boost_random.html Boost Random Number Library]&lt;br&gt;<br /> More information on the [http://tclap.sourceforge.net/ TCLAP Library]<br /> <br /> == Documentation ==<br /> <br /> [[Media:Fte_Document_06012012.pdf‎ | User's guide]]</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=FTEC&diff=4196 2012-01-12T20:27:09Z

<p>Mreppell: </p> <hr /> <div>fte is a coalescent simulation program developed by Mark Reppell, Michael Boehnke, and Sebastian Zöllner capable of modeling samples drawn from a population which has undergone faster than exponential growth.<br /> <br /> ==Installation and Compilation==<br /> <br /> 1) Download the appropriate .tar file below &lt;br&gt;<br /> 2) Place downloaded file in the directory where you would like the program to reside and untar the file &lt;br&gt;<br /> 3) Inside the new directory /fte which has been created enter the command 'make' &lt;br&gt;<br /> 4) An executable file named 'fte' should now reside in this directory, this is the simulator and can be run using './fte -parameters'.<br /> <br /> For information on how to use the simulator see the user's guide below.<br /> <br /> == Download ==<br /> <br /> fte requires header files from both the Boost and TCLAP libraries to compile and run. There are 3 available downloads below, differing in which of these library files they contain. File size and download time increase with the inclusion of each set of library files, so a user can select the most appropriate download for their system. If a user's system already includes a library and they download a version of fte that includes the library's header files the program will compile without problem, so if there is any uncertainty download the larger source file below.<br /> <br /> [[Media:Fte_v1.36.tar‎| Program files with both Boost and TCLAP header files (50 Mb) ]] &lt;br&gt;<br /> [[Media:Fte_v1.36_noboost.tar | Program files with TCLAP header files (270 Kb)]] &lt;br&gt;<br /> [[Media:Fte_v1.36_src_only.tar | Program files without Boost or TCLAP header files (80 Kb)]] &lt;br&gt;<br /> <br /> <br /> More information on [http://www.boost.org/ Boost] and the [http://www.boost.org/doc/libs/1_48_0/doc/html/boost_random.html Boost Random Number Library]&lt;br&gt;<br /> More information on the [http://tclap.sourceforge.net/ TCLAP Library]<br /> <br /> == Documentation ==<br /> <br /> [[Media:Fte_Document_06012012.pdf‎ | User's guide]]</div>

Mreppell http://genome.sph.umich.edu/w/index.php?title=FTEC&diff=4195 2012-01-12T19:27:38Z

<p>Mreppell: </p> <hr /> <div>fte is a coalescent simulation program developed by Mark Reppell, Michael Boehnke, and Sebastian Zöllner capable of modeling samples drawn from a population which has undergone faster than exponential growth.<br /> <br /> ==Installation and Compilation==<br /> <br /> 1) Download the appropriate .tar file below &lt;br&gt;<br /> 2) Place downloaded file in the directory where you would like the program to reside and untar the file &lt;br&gt;<br /> 3) Inside the new directory /fte which has been created enter the command 'make' &lt;br&gt;<br /> 4) An executable file named 'fte' should now reside in this directory, this is the simulator and can be run using './fte -parameters'.<br /> <br /> For information on how to use the simulator see the user's guide below.<br /> <br /> == Download ==<br /> <br /> fte requires header files from both the Boost and TCLAP libraries to compile and run. There are 3 available downloads below, differing in which of these library files they contain. File size and download time increase with the inclusion of each set of library files, so a user can select the most appropriate download for their system. If a user's system already includes a library and they download a version of fte including that library's header files the program will compile without problems, so if there is any uncertainty download the larger source file below.<br /> <br /> [[Media:Fte_v1.36.tar‎| Program files with both Boost and TCLAP header files (50 Mb) ]] &lt;br&gt;<br /> [[Media:Fte_v1.36_noboost.tar | Program files with TCLAP header files (270 Kb)]] &lt;br&gt;<br /> [[Media:Fte_v1.36_src_only.tar | Program files without Boost or TCLAP header files (80 Kb)]] &lt;br&gt;<br /> <br /> <br /> More information on [http://www.boost.org/ Boost] and the [http://www.boost.org/doc/libs/1_48_0/doc/html/boost_random.html Boost Random Number Library]&lt;br&gt;<br /> More information on the [http://tclap.sourceforge.net/ TCLAP Library]<br /> <br /> == Documentation ==<br /> <br /> [[Media:Fte_Document_06012012.pdf‎ | User's guide]]</div>

Mreppell