How to define a pathfile for TrimAl command "trimal -compareset pathfile -out output4"

Question

[laz84]

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!

Answer 1

[scapella]

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.

[laz84]

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.

[scapella]

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