1 answer
The instructions you need to follow, to run PAML programs under windows, are found here:
http://abacus.gene.ucl.ac.uk/software/paml.html
You need to read the section "Downloading and Setting up PAML" and then subsection "Windows 9x/NT/2000/XP/Vista/7"
This info may be missing from the manual, so have a go at looking through this stuff if you've not tried it already.
Note that there is no "program" called "paml" or "PAML", rather you run individual programs within the PAML packaged (in your case it would be codeml)
I've never used PAML under windows, but I think the idea is the same as under *nix i.e. the instructions about which data file to use, and which paramenters to run the analysis with, are specified in a "control" file that you set up (and give an appropriate name to) prior to running the programs
It depends. Probably you do need to modify the control file each time, otherwise you will always be running codeml with the same input file (name) and output file (name) - although I guess you could run a pipeline where you:
set up infile and outfile name in the control file
provide approrpiate infile content
run codeml
rename outfile to an appropriate name
provide codeml with differnet input by renaming a file to the name of the infile in your control file
run codeml
repeat
This way you could process a set of different datafiles using the same set of parameters, without having to edit the control file each time
@aiden-budd: see this question. link : Phylogenetic Analysis By Maximum Likelihood (Paml) : Upon Phylip Input Yn00.Clt Program Not Running.
Log in to answer this question.
-
Selection Pressure Analysis
written by upasana •
-
What is the importance of partitions in phylogenomics analysis ?
written by sunnykevin97
-
How codeml detects positive selection
written by Amay •
-
Positive selection analysis on gene family using the PAML package
written by farahbakhsh.sara •
-
Sites under selection by PAML have conserved amino acid
written by urjaswita
-
PAML CodeML Branch Site Model for Positive Selection
written by courtney1cheng •
-
PAML CodeML Branch Site Model for Positive Selection
written by courtney1cheng •
-
Detect Positively Selected Sites Among A Lineage In Paml
written by yangzhenzhen1988 •
-
Phylogenetic Analysis By Maximum Likelihood (Paml) : Upon Phylip Input Yn00.Clt Program Not Running.
written by Naren
-
Paml - Branch-Site Models
written by Kartik Sunagar
We need some more information. What have you tried and what errors are you getting?
Phylogenetic Analysis By Maximum Likelihood (Paml) : Upon Phylip Input Yn00.Clt Program Not Running.