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Methodology Questions >> How to >> Are my indices consistent with HyPhy? http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1349350424 Message started by Mawa Jekot on Oct 4th, 2012 at 4:33am |
Title: Are my indices consistent with HyPhy? Post by Mawa Jekot on Oct 4th, 2012 at 4:33am
Hi
My data consists of sequences that have a 0 or 1 indicator before each codon. For example, 0ACT1GAG. I use $BASESET:"ACGT01" in my data file and exclude the attached "exclusions.txt" combinations in my filter. These exclusions are any combination of length four of A, C, G, T, 0 and 1 which does not have a 0 or 1 indicator in the first position and 3 nucleotides in the following three positions. It also contains the stop codons, six in total (0TAA,0TAG,0TGA and 1TAA,1TAG,1TGA). The rate matrix (122 x 122) I specify for the model assumes the indices are coded as follows: 0 = 0AAA 1 = 0AAC 61 = 1AAA 121 = 1TTT Is this consistent with how HyPhy expects it? Thanks http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?action=downloadfile;file=Exclusions.txt (5 KB | 1
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Title: Re: Are my indices consistent with HyPhy? Post by Sergei on Oct 8th, 2012 at 11:42am
Hi Mawa,
This seems correct. When you create the datafilter, you can perform a sanity check to ensure that the encoding is correct. See attached (it is a self-contained NEXUS + HyPhy BF file). Sergei http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?action=downloadfile;file=CheckEncoding.bf (11 KB | 1
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