Hello everyone,
I have read articles published in good journals which have used PAML for phylogenetic analysis with around 100 sequences. But in PAML manual, it is written that PAML should not be used for more than 10 sequences.
What do you suggest?
If no, then which other program can be used?
Thank you in advance!
Try IQ-tree
http://mbe.oxfordjournals.org/content/early/2014/11/03/molbev.msu300
or FASTDNAML, RAXML, etc.
http://sco.h-its.org/exelixis/web/software/raxml/
The webpage of IQ-TREE is: http://www.cibiv.at/software/iqtree/
IQ-TREE offers a huge collection of up-to-date models including also partition models and free-rate models, a model-testing to determine the best-fit model(s) for your data without needing additional software, a fast implementation of the ML framework and the ultrafast bootstrap approximation.
About the 10-sequences limit in PAML - I knew that for codon models. Hence, often user given trees where analyzed after being reconstructed with other software.
Codon models are also implemented in IQ-TREE and can be used for tree search as well.
All 3 software packages mentioned above by Brian can deal with many more than 100 sequences.
And I think also IQ-TREE's web interface can cope with more than 100 sequences as input.
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