Hi! I'm using commandline version of TrimAl to trim aligned sequences.
I want to compare 4 alignments created by different methods through the command trimal -compareset <pathfile> -out output4.
However, after reading tutorial and explanation, still don't know what is a pathfile. Could anyone tell me how to define and format a pathfile for trimal?
Thanks very much!
Hi there,
The -compareset option has been developed to compute the sum-of-pairs score, which we called consistency, among two or more alignments and, therefore, 1) select the most consistent alignment and/or 2) trim those columns with a consistency score lower than a given threshold. We also implemented the option of choosing an specific alignment (-forceselect) as the most consistent one, compute the consistency score using other alignments and trim it.
To use all this functionality, you have to provide a file which contains the path of those alignments you want to be compared. Let say you want to compare <alig_1>, <alig_2> and <alig_3> then the input file (paths-file) should like this:
<absolute or relative path to alig_1>
<absolute or relative path to alig_2>
<absolute or relative path to alig_3>
I hope it helps.
S
PS: We are working on an improved version of trimAl manual & documentation which we expect to release by the end of this year/beginning of 2015.
Thanks very much, Mr. Capella-Gutierrez.
While I defined the pathfile in three format below, using Ultraedit32.
format1: (in bin of TrimAL)
143Tcoffee.fas
143Clustal.fas
143Muscle.fas
143Mafft.fas
format2:(in D:)
D:\143Tcoffee.fas
D:\143Clustal.fas
D:\143Muscle.fas
D:\143Mafft.fas
format3:(in D:)
<D:\143Tcoffee.fas>
<D:\143Clustal.fas>
<D:\143Muscle.fas>
<D:\143Mafft.fas>
Still, error:
Alignmant not loaded:"" check the file's content.
It seems strange - could you contact me at the email address provided at trimal.cgenomics.org.
My first guess is it may be related to a really old version of the program. When contacting me, it would be nice if you can tell me which version you are using.
Cheers!
S
That's why I'm here to contact you. I searched trimal.cgenomics.org thoroughly, and there no any contacting method, except leaving my email.
please contact me, laz84@163.com
Just for other readers.
We can be contacted at http://trimal.cgenomics.org/trimal_team where there is information about the current development team.
I'm writing to you privately.
S
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