add flag to write out bootstrap msa from main run #125
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After initial PR I realized this requires one more tweak so raxml-ng only writes out the number of bootstrap alignments it used. If we set the maximum number of replicates to 1,000 but it converges after 250, the code now writes out 250 alignments, not 1,000. |
amkozlov
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Sep 8, 2021
…ence run (PR #125, thanks to @harmsm) Squashed commit of the following: commit f5056c33f6c10e951599434e530b1d774263789d Author: Alexey Kozlov <alexey.kozlov@h-its.org> Date: Wed Sep 8 16:28:52 2021 +0200 minor style corrections commit d5e43e4 Author: harmsm <harmsm@gmail.com> Date: Wed Aug 11 18:35:14 2021 -0700 only write out number of bootstrap alignments used commit 05df874 Author: harmsm <harmsm@gmail.com> Date: Wed Aug 11 16:59:32 2021 -0700 added error check to make sure bootstraps being generated commit 1f2906b Author: harmsm <harmsm@gmail.com> Date: Wed Aug 11 16:47:55 2021 -0700 added option to write all bootstrap msa
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Thanks Mike, I just merged it into master manually with minor changes! |
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It would be extremely useful if raxml-ng could write out bootstrap multiple sequence alignments from tree building runs (e.g.
--all). Although the--bsmsamode allows a user to write out bootstrap alignments, doing subsequent tree building on these alignments loses the fast parallelization native to raxml-ng/libpll. I'd like to run--alland be able to get a stack of bootstrap trees and alignments I can then use for downstream analyses.I implemented a new flag (
--bs-write-msa) that causes raxml-ng to call the code block under control ofCommand::bsmsa, thus writing out the bootstrap replicate alignments after tree creation. The new flag sets a newwrite_bs_msaboolean I added to the main opts data structure. I added a doc string to the command line argument and an error check to make sure the flag is only invoked if bootstrap replicates are being generated.Not sure if there I should merge into dev or master. (It looked like dev was stale). Let me know if I should change PR branches.
Thanks for great package and for considering PR.