Dear all,
I want to use PAML for Checking positive selection by dn/ds calulation.
I am using Phylip alignment file. (Which PAML suggests to be used as input).
This is my input Phylip file.
7 1065 MPREF94h99 ---------- ---------- ---------- ---------- ---------- MPREF9b499 ---------- ---------- ---------- ---------- ---------- MPREF03499 ---------- ---------- ---------- ---------- ---------- MPREF949l9 AGCGAAAAAA GTTTTAAACG TTGAAAGCTC CTATCTAGAT AATATGATTC MPREF9c499 ---------- ---------- ---------- ---------- ---------- MPREF949d9 ---------- ---------- ---------- ---------- ---------- MPREF0t349 ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- TTTGGGGTAA ACGCCCCTTG ATAGATTCTA TCAACGATAT TAAAGATTAC ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- -------TTG AAAATATTGT TATATTTTGA AGGTGAGAAA ATCTTAGCTA
And this is cmd error message.
C:\Users\Lenovo\Desktop\dnds\PAML\paml4.6>yn00 YN00 in paml version 4.6, August 2012
Reading options from yn00.ctl..
ns = 7 ls = 1065 Reading sequences, sequential format..
Error in sequence data file: P at 52 seq 1. Make sure to separate the sequence from its name by 2 or more spaces.
(Note : there are more than two spaces between name and sequence in my file)
C:\Users\Lenovo\Desktop\dnds\PAML\paml4.6>
I am not getting output after running file yn00.clt
What may be the problem?
2 answers
I actually run codeml and baseml using interleaved files with the header formatted like that (with an "I"). This was pointed out to me by a colleague about 5 years who had a script what would just do this simple reformatting. There may be other issues with the file, but this formatting works for me.
Thanks SES: i did that now I'm getting this msg:
C:\Users\Lenovo\Desktop\dnds\PAML\paml4.6>yn00 YN00 in paml version 4.6, August 2012
Reading options from yn00.ctl.. ns = 7 ls = 1065 Reading sequences, interlaved format.. Counting site patterns.. 0:00 26 patterns at 26 / 26 sites (100.0%), 0:00 stop codon TAA in seq # 1: MPREF94h99 codons in other sequences are seq # 1 MPREF94h99 TAA seq # 2 MPREF9b499 TGA seq # 3 MPREF03499 TTC seq # 4 MPREF949l9 TGC seq # 5 MPREF9c499 TGC seq # 6 MPREF949d9 GAA seq # 7 MPREF0t349 TGA
This might help: http://bit.ly/1utdbFg it converts FASTA alignment file to a non-interleaved/sequential Phylip format :)
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you are sure they are spaces and not tabs?
yeah! as in original file, there was only one space. I inserted them with notepad.