RAxML can't, parse the alignment file as phylip file it will now try to parse it as FASTA file

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Joker Leo

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Jul 1, 2022, 3:53:12 AM7/1/22

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Dear author:

when I using standard-RAxML-8.2.12,having a problem:

【RAxML can't, parse the alignment file as phylip file it will now try to parse it as FASTA file】

could you help me ,thank you

Grimm

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Jul 1, 2022, 8:38:47 AM7/1/22

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Hi jk_...,

this just means your MSA has the wrong input format. Please check the manual for guidelines for the supported formats by classic RAxML.

The standard extended phylip format used by RAxML looks like this

4 10

taxon1 GGGGGACGTG

taxon2 AGAGSACGTC

taxon3 GGAGTACCTC

taxon4 GGTTTAGCTC

First number first row is the number of tips/OTUs/accessions, second number the number of characters (nucleotide, amino acid or multistate: 0,1,2,...)

"Extended" means the length of the taxon name can be longer than 10digits, which was the limit of classic PHYLIP.