Computing species tree with RaxML

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Sam

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Apr 14, 2015, 3:26:37 AM4/14/15
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I have >900 ortholog proteins groups of six metazoans. I concatenated the single copy ortholog in concat_alignments.fa and now want to infer a species tree by using this alignment.
What will be the BEST option to compute such tree?

I run the RaxML with the following option
raxmlHPC-PTHREADS-AVX -f a -T 2 -p 12345 -m PROTGAMMAAUTO -x 12345 -# 1000 -s concat_alignments.fa -m PROTGAMMAAUTO -n T20
Please suggest what should I do next? I read the manual but bit confused.
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