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Methodology Questions >> How to >> Defining custom alphabets for sequence data. http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1116863541 Message started by Sergei on May 23rd, 2005 at 8:52am |
Title: Defining custom alphabets for sequence data. Post by Sergei on May 23rd, 2005 at 8:52am
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HyPhy can be told to interpet character data using a custom alphabet by specifying the details in an alignment file. FASTA and PHYLIP formats do not directly provide a mechanism for defining a new character set, but HyPhy has custom instructions for this. The little fragment below shows an alignment of 3 sequences on three characters (A,B and C) and a gap character: Code (] $BASESET:"ABC" $TOKEN:"-"="ABC" >seq1 AABBCC >seq2 A-BBAC >seq3 CABBCC [/code):
Datafiles like this can be read and filtered by HyPhy and if one defines a 3 state rate matrix for the above example, e.g. rateMx = [*,a,b} {a,*,c} {b,c,*], (here an i,j entry is the rate of substituting character i with chartacter j, i,j=0..2. In the example above 'A' has code 0 since it was listed first, 'B' has code 1 and 'C' has code 2), then a model can be fitted by ML. HTH, Sergei |
Title: Re: Defining custom alphabets for sequence data. Post by Steven on May 24th, 2005 at 3:10am
Thanks so much
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