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Commits on Aug 26, 2020

• added missing include, removed explicit install of flex/bison during macos CI

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• removed pedantic-errors since clang doesnt play well with anonymous unions (libpll issue)

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Commits on Jun 24, 2020

• added a bunch of failure guards around pll functions

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• added missing semicolon

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• added failure guards to set_tip_states

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• swapped outputs of model parameters, always show the one actually being used after epirical base freq calculation

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• fixed --split, read_any_seqfile function to actually work with fasta.gz

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Commits on Mar 6, 2020

• fixed a host of issues unearthed by softwipe

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Commits on Oct 21, 2019

• updated the help text regarding the split command producing two files now

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Commits on Jun 25, 2019

• added automated parsing of model params from iqtree log files, imporved parsing of raxml-8 files (added p_inv)

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Commits on Jun 24, 2019

• added much better check to reference tree/msa mismatch

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Commits on Jun 5, 2019

• updated CLI11 to version 1.8

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Commits on May 22, 2019

• --split: added output of reference file, added automatic detection of query/reference alignment width discrepancies

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Commits on Mar 18, 2019

• added support for reading fasta files for --split (issue #28)

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Commits on Feb 22, 2019

• added preservation of inner node labels

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Commits on Feb 6, 2019

• rate scalers option ignore casing

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Commits on Feb 1, 2019

• fixed #25 (incorrectly sorted output leading to slight variations in results)

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Commits on Jan 10, 2019

• added option to toggle root preservation

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• fixed incorrect assignment of tip sequences to clvs under rooted trees

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Commits on Jan 9, 2019

• added more sensible autodetection of RAxML 8 infofile

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Commits on Dec 18, 2018

• added --redo option a la raxml-ng

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• Merge branch 'master' into dev

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  7672ee8

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• fix for incorrect handling of empirical base freqs from raxml-ng model string

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  16cd3b7

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• added missing header (issue #22)

  

  Pierre Barbera

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  12d55fa

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• very basic modelfile type detection and parsing

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Commits on Dec 12, 2018

• Merge branch 'master' into dev

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• added string header to rtree_mapper re: issue #22

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• added option to toggle per rate scalers, added some CLI synonyms

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Commits on Dec 11, 2018

• automatic use of per rate scalers

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Commits on Dec 4, 2018

• Merge branch 'master' of github.com:Pbdas/epa-ng

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  8b2e764

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• fixed a small error in candidate selection

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• replaced exception with a warning for non-exact reference files

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Commits on Nov 29, 2018

• Merge branch 'master' of github.com:Pbdas/epa-ng

  

  Pierre Barbera

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• added support for reading interleaved phylip files for the reference msa argument of --split

  

  Pierre Barbera

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Commits on Nov 28, 2018

• fixed missing header producing errors only in very specific clang versions

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