1.0.6

• fixed issue where version format is not clearly parsed.
• added option to enter genetic code.

1.0.5

• added print statement that describes the run
• minor: updated reference file in test CTL files
• fixed bootstrap bug. It was bootstrapping if N>0
• prints package Version with every run now
• BWA is the default aligner now.

1.0.4: Merge pull request #6 from LANL-Bioinformatics/master

• now makes phylogeny from core genome as default.

1.0.3

• Now added output folders that stores alignment files, tree files, etc. separately
• Added IQ-tree as a third option for conducting phylogenetic analysis

1.0.2

• split summarystatistics.txt table to multiple tables
• changed how comparesketch was called
• changed log file name to just project.log from project_phame.log
• changed main script to phame from runPhaME
• now also outputs alignment with all invariant sites

1.0.1

• Fixed a bug that was incorrectly parsing version number of FastTree

1.0.0

• First version released.

santosh

• changes with installation requirements

saroj

pre-release

rajesh

• the release now effectively uses mash to select genome based on ANI
• readstoGenome.pl script now uses the specified thread, before it was using 8, no matter what was specified
• PAML, if installed correctly works for the genes, and gives a nice table with dN/dS ratio and corresponding L score.
• PAML now uses RaxML tree even if FastTree is selected. RaxML tree is made for PAML analysis
• HyPhy installation script added, which is still having a bit of problem, but once installed correctly, it can run few Hyphy modules. It only, however, includes the genes that do not have any gaps in the alignment.
• Dockerfile is added. Dockerized version can be used.