MSAs and tree inference results

This archive contains data and code used to produce the results for the following preprint:

Alexey M. Kozlov, Diego Darriba, Tomáš Flouri, Benoit Morel, and Alexandros Stamatakis (2018)
RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference.
bioRxiv.
https://www.biorxiv.org/content/early/2018/10/18/447110


INPUT DATA
----------

/data Multiple sequence alignments, partition files and starting trees

For historical reasons, directory/file names are slightly different
from the dataset names used in the paper.

Please see the mapping below:

Paper Directory/file name
------ ---------------------
SongD1 dna_rokasD1
MisoD2a dna_rokasD2a
MisoD2b dna_rokasD2b
WickD3a dna_rokasD3a
WickD3b dna_rokasD3b
XiD4 dna_rokasD4
PrumD6 dna_rokasD6
TarvD7 dna_rokasD7
PeteD8 dna_hymeALL
ShiD9 dna_ShiD9
StamD10 dna_StamD10

NagyA1 aa_rokasA1
MisoA2 aa_rokasA2
WickA3 aa_rokasA3
ChenA4 aa_rokasA4
StruA5 aa_rokasA5
BoroA6 aa_rokasA6
WhelA7 aa_rokasA7
YangA8 aa_rokasA8
ShenA9 aa_rokasA9
KatzA10 aa_rokasA10p
GitzA12 aa_GitzA12


Please cite original publications when (re-)using the datasets,
see Table 3 in RAxML-NG supplement for details!

Most matrices were obtained via (Zhou et al. 2018):

https://figshare.com/projects/Evaluating_fast_maximum_likelihood-based_phylogenetic_programs_using_empirical_phylogenomic_data_sets/22040


RESULTS
-------

raxml/ RAxML runs
examl/ ExaML runs
iqtree/ IQTree runs
raxng/ RAxML-NG runs
lheval-iq-blo/ Tree likelihood re-evaluation with IQTree (with re-optimizing branch lengths)
scripts/ Misc. scripts used to submit cluster jobs, collect results etc.
plots/ R scripts to produce plots for supplement Figures 2 to 5