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iqtree / iqtree2

NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
GNU General Public License v2.0
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Matching Gene Trees in Treefile to Alignment File Names #327

Open simone-says opened 1 month ago

simone-says commented 1 month ago

Discussed in https://github.com/iqtree/iqtree2/discussions/323

Originally posted by **simone-says** September 22, 2024 Is the order of the gene trees output in the *.treefile the same order that the alignment files are read in, or the same order that is output into the log file during partition testing? I need to match individual gene trees to the alignments that made them, but there are no unique identifiers preserved in the *.treefile. This is the command used to make the gene trees: `iqtree2 -S /projects/busco_phylo/results/03_trimal/03_realigned_trim2/UCEs/05_unsat --prefix UCEs_unsat.loci -T AUTO`
simone-says commented 3 weeks ago

If there is no conserved order to how the gene trees are output then I can try to work on a script to match them after running, but I would like to know before I jump down another rabbit hole :)