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This repository has been archived by the owner on Feb 6, 2024. It is now read-only.
(This is low priority as there is an obvious workaround.)
I downloaded an alignment and tree from TreeBase. Annoyingly, some of
the taxon names contain spaces, and use quotes around them. IQtree reads
the alignment OK, doing some auto-substitutions to deal with space and
quote characters. The problem is then when it reads the tree file, it
doesn't do the same auto-substitutions, so it can't reconcile the
alignment taxa with the tree taxa.
(This is low priority as there is an obvious workaround.)
I downloaded an alignment and tree from TreeBase. Annoyingly, some of
the taxon names contain spaces, and use quotes around them. IQtree reads
the alignment OK, doing some auto-substitutions to deal with space and
quote characters. The problem is then when it reads the tree file, it
doesn't do the same auto-substitutions, so it can't reconcile the
alignment taxa with the tree taxa.
./iqtree -s M39346.fasta -te T100530.treefile -redo -m 012345
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