Phylogenetic Analysis By Maximum Likelihood (Paml) : Upon Phylip Input Yn00.Clt Program Not Running.

Question

[Naren]

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?

[Whetting]

you are sure they are spaces and not tabs?

[Naren]

yeah! as in original file, there was only one space. I inserted them with notepad.

Answer 1

[Whetting]

It looks like PAML is looking for a sequential file "ns = 7 ls = 1065 Reading sequences, sequential format..".
However, you are providing an interleaved file. Try converting it to sequential and see what happens

[SES]

Changing the header to " 7 1065 I" may be an easier test of the format. That should tell the program it's interleaved.

[Whetting]

PAML is really finicky...I am not sure that will work, but it is worth the shot

[SES]

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.

[Whetting]

I stand corrected...and that is good to know

[Naren]

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

[Whetting]

PAML does not like stop codons. Are these stopcodons internal or terminal? If terminal just remove them. If they are internal, you may need to rethink your analysis...

Answer 2

[zeeefa]

This might help: http://bit.ly/1utdbFg it converts FASTA alignment file to a non-interleaved/sequential Phylip format :)