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ddarriba / jmodeltest2

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What input formats are accepted? #45

Open rsharris opened 1 year ago

rsharris commented 1 year ago

In the PDF manual for v2.1.10, section 6.1 Converting Alignment Files says: "jModelTest accepts several input alignment file formats ..."

It would be helpful to know which alignment file formats it accepts. I have an alignment in MAF (http://genome.ucsc.edu/FAQ/FAQformat#format5) which is a quite common format. But I ran a small example and my input file was rejected.

So it seems my only options are to make my input look like example-data/aP6.fas, or to dig through the code to figure out what other formats might be accepted.

In particular, I have several independent alignment blocks, each with aligned sequence for 7 species (the same 7 in all blocks). It's not clear how to make that look like looking at example-data/aP6.fas.

liamxg commented 1 year ago

@rsharris fasta format is okay.

rsharris commented 1 year ago

@liamxg Doesn't really address what I wrote in my last paragraph. Should I concatenate the sequences from the independent blocks? Should I put an N between each pair?