Question: Phylogenetic Analysis By Maximum Likelihood (Paml) : Upon Phylip Input Yn00.Clt Program Not Running.
0
gravatar for Nari
5.8 years ago by
Nari860
United States
Nari860 wrote:

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?

paml • 6.2k views
ADD COMMENTlink modified 3.9 years ago by zeeefa80 • written 5.8 years ago by Nari860

you are sure they are spaces and not tabs?

ADD REPLYlink written 5.8 years ago by Whetting1.5k

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

ADD REPLYlink modified 5.8 years ago • written 5.8 years ago by Nari860
2
gravatar for Whetting
5.8 years ago by
Whetting1.5k
Bethesda, MD
Whetting1.5k wrote:

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

ADD COMMENTlink written 5.8 years ago by Whetting1.5k
1

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

ADD REPLYlink modified 5.8 years ago • written 5.8 years ago by SES8.1k

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

ADD REPLYlink written 5.8 years ago by Whetting1.5k
3

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.

ADD REPLYlink modified 5.8 years ago • written 5.8 years ago by SES8.1k

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

ADD REPLYlink written 5.8 years ago by Whetting1.5k

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

ADD REPLYlink written 5.8 years ago by Nari860
1

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...

ADD REPLYlink written 5.8 years ago by Whetting1.5k
0
gravatar for zeeefa
3.9 years ago by
zeeefa80
Sverige
zeeefa80 wrote:

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

ADD COMMENTlink written 3.9 years ago by zeeefa80
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