HybPhyloMaker v1.6.4

Several new features/options were included

• combination of summary tables in XLSX format (a new script)
• alternative consensus calling with ambiguous bases and its processing
• selection of loci with low heterozygosity (possible exclusion of paralogue/chimeric sequences)
• more option for RAxML gene trees calculation (model selection - GTRGAMMA or GTRCAT, bootstrap - standard or rapid, number of bootstrap replicates, bootstopping option)
• BUCKy concordance tree
• modified test dataset
• all scripts are nearly fully working on Smithsonian HPC (Hydra)
• installation of BCFtools added to install_software.sh
• updated manual
• updated 'settings.cfg'

HybPhyloMaker v1.5

• raw reads are gzipped after processing (1)
• BWA added as alternative mapping method (2)
• bugs removed (4, 5, 6a)
• rooting is done by 'nw_reeroot -s' now (7, 8), most recent version of NewickUtilities from GitHub is necessary now!
• possibility to collapse unsupported branches & subselect gene trees before running species tree estimations (10)
• updated manual
• updated 'settings.cfg'
• much improved 'install_software.sh' script (does not re-install software that is already installed)

HybPhyloMaker v1.4.2

• updated manual
• adapted for PBS Pro submission system on MetaCentrum
• user-provided adapter file for trimming
• summary table after read mapping
• a newer version of ASTRAL (4.11.1)

HybPhyloMaker v1.4

Changes in this release:

• kindel is now used for consensus calling (OCOCO is still an option)
• exons can be put into the correct reading frame (and translated to AA) - new script 4b
• all subsequent scripts implements the option for work with frame corrected data
• gene trees can be constructed with partitioning (by exon or by codon position)
• RAxML tests for completely invariable sites and use the reduced dataset if necessary
• new settings (work with frame corrected data, gene partitioning, consensus calling)
• new software is required and its installation added to install_software.sh (kindel, EMBOSS)

HybPhyloMaker v1.3

Read mapping and consensus calling implemented. Scripts re-numbered. 'install_software.sh' for easy install of all necessary software. Several bugs fixed.

HybPhyloMaker v1.2

v.1.2.0.