Bio::Tools::Run::Phylo::Phyml Lacks LG model of AA sequence evolution

[cjfields]

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Author Name: Jessen Bredeson (Jessen Bredeson)
Original Redmine Issue: 3226, https://redmine.open-bio.org/issues/3226
Original Date: 2011-05-02
Original Assignee: Bioperl Guts

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Page 12 of the PhyML 3.0 manual (at http://www.atgc-montpellier.fr/download/papers/phyml\_manual\_2009.pdf) states that the executable supports the LG model of sequence evolution and is the default amino acid substitution model, however the current version of the Bio::Tools::Run::Phylo::Phyml wrapper does not reflect this.

Attached is a ‘git diff’ of my and the available bioperl-run module.

Enjoy
Jessen