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fix bootstrap trees printing to a file for --bs-metric ps and --bs-me…

amkozlovpushed 3 commits to dev • d2a4764…ea7102a • 
yesterday

new branch support metrics: parsimony support (--bs-metric ps), parsi…

amkozlovpushed 4 commits to dev • 9c40cd4…d2a4764 • 
6 days ago

new branch support metrics: parsimony support (--bs-metric ps), parsi…

amkozlovpushed 1 commit to ebg • a6c3bfd…d2a4764 • 
6 days ago

EBG: cleanup, allow to specify number of parsimony bootstrap trees vi…

amkozlovpushed 1 commit to ebg • fa54f27…a6c3bfd • 
7 days ago

EBG: fix wrong feature order, remove debug output

amkozlovpushed 1 commit to ebg • 9111ad7…fa54f27 • 
8 days ago

Add Educated Bootstrap Guesser support (WIP). Usage: --bs-metric ebg

amkozlovcreated ebg • 9111ad7 • 
15 days ago

allow to exclude MSA sites from the analysis (#189)

amkozlovpushed 1 commit to dev • 8ad1683…9c40cd4 • 
on Jan 17

auto-partitioning with parameter linkage, e.g. GTR/C4 = 4 partitions …

amkozlovpushed 1 commit to dev • 021c458…8ad1683 • 
on Jan 15

add ARM NEON support, allow to build a portable binary (cmake -DPORTA…

amkozlovpushed 1 commit to dev • 02b3d9e…021c458 • 
on Jan 9

fix edge case for auto-partitioning

amkozlovpushed 2 commits to dev • c43144a…02b3d9e • 
on Dec 11, 2024

pythia: add missing features (patterns_per_site, pattern_entropy)

amkozlovpushed 1 commit to dev • 3a8775b…c43144a • 
on Nov 28, 2024

GTest now requires c++14, make it happy

amkozlovpushed 1 commit to dev • ecdf971…3a8775b • 
on Nov 21, 2024

check that constraint tree has at least 4 taxa and print a clear erro…

amkozlovpushed 1 commit to dev • e12b46b…ecdf971 • 
on Nov 21, 2024

upgrade difficulty prediction to Pythia v1.2

amkozlovpushed 1 commit to dev • 97dda13…e12b46b • 
on Oct 31, 2024

update README

amkozlovpushed 1 commit to dev • 3154fd6…97dda13 • 
on Oct 24, 2024

fix unit tests

amkozlovpushed 58 commits to dev • 12fa8ba…3154fd6 • 
on Oct 24, 2024

adaptive: support per-rate scalers in ancestral state reconstruction

amkozlovpushed 2 commits to adaptive • c726f3b…a663446 • 
on Oct 23, 2024

small improvements to SH-aLRT; add --opt-topology option to choose tr…

amkozlovpushed 1 commit to adaptive • b721197…c726f3b • 
on Oct 2, 2024

implement SH-aLRT branch support (usage: --bs-metric sh)

amkozlovpushed 3 commits to adaptive • f755493…b721197 • 
on Oct 1, 2024

adaptive: disable pythia if command cannot use difficulty score (eg -…

amkozlovpushed 1 commit to adaptive • f20e498…f755493 • 
on Sep 10, 2024

add raxml8-style rapid bootstrapping (--bs-metric rbs), still require…

amkozlovpushed 1 commit to adaptive • 5e4f283…f20e498 • 
on Aug 30, 2024

adaptive: parallel parsimony bugfix

amkozlovpushed 1 commit to adaptive • ff5a630…5e4f283 • 
on Aug 28, 2024

adaptive: add --pythia command: print MSA difficulty score

amkozlovpushed 1 commit to adaptive • 833cfc8…ff5a630 • 
on Aug 28, 2024

adaptive: add coarse-grained parallelization of parsimony, reuse pyth…

amkozlovpushed 2 commits to adaptive • 366d9d1…833cfc8 • 
on Aug 27, 2024

fix compilation error

amkozlovpushed 1 commit to adaptive • 6543291…366d9d1 • 
on Aug 25, 2024

add entropy-based auto-partitioning (usage: '--model GTR/P5', '--mode…

amkozlovpushed 4 commits to adaptive • b1b9aa5…6543291 • 
on Aug 1, 2024

bump version number, update download links

amkozlovpushed 1 commit to master • 941e0e6…805318c • 
on Apr 30, 2024

remove IDE files

amkozlovpushed 1 commit to master • aac24a5…941e0e6 • 
on Apr 30, 2024

improve CPU core count detection in node-sharing scenario (check sche…

amkozlovpushed 1 commit to master • a523a3f…aac24a5 • 
on Apr 30, 2024

fix MPI build

amkozlovpushed 2 commits to adaptive • 72d740f…b1b9aa5 • 
on Apr 11, 2024