v1.3

--best_fit to specify branch length estimation under the fixed, best-fitting substitution model, during bootstrap. this better matches the behaviour of mcmctree's approximate likelihood approach for divergence time and rate MCMC updates.

v1.2

• A bug in re-ordering the tip name is fixed. Basically, now all characters are made lowercase when ordering the tip name.

• in case a sequence contains only gaps, the first gap will be replaced by "A" to ensure bootstrap in iqtree works.

• By default, -mwopt is specified for IQ-Tree (more details about why see Banos et al 2024). If you would like to turn this option off, use --no_mwopt.

Thanks Charley McCharley for bug report.

v1.1

the updated version completely according to the PR from Sandra. see details in Issue

particularly thanks to @sabifo4 for testing v1.0 of the tool and many efforts in contributing to making the tool much more user-friendly. thanks also to @ERRMoody for testing.

v1.0

the first version. no change to the content since 2023.07. but note also that the README file is not clear in regards to installation of some necessary Ruby packages, as pointed out by sandra alvarez.