v0.1.9

• Added gotree collapse depth command to collapse branches that have a given depth
• Added gotree resolve command, to randomly resolve multifurcations, by adding 0 length branches
• Added gotree annotate command, to annotate (name) internal nodes (lca) of a tree, given group of tips
• Added option to gotree prune to remove individual tips given on command line
• Corrections:
  • Unroot can take a multi tree file
  • Corrected Makefile
  • gotree compare edge can display species that are different for each compared branch

v0.1.8

• Added clear pvalues command to clear support pvalues from input trees
• Changed cutoff for branch support collapsing: Strict "<" now
• Added to locality measure to stats edges command
• Corrected bug in pvalue assignment
• Added information about number of times each taxon is moved when computing transfer support
• Bug corrections:
  • Corrected bug in compare edges command
  • Logs are written to stderr by default for compute support...

v0.1.7

• rename command can now take a file containing several trees
• Added matrix command, that prints the distance matrix equivalent to the input tree
• Added randsupport command, that attributes random supports to branches of the input tree
• Bug fixes:
  • Corrected seed in randbrlen command

v0.1.6

• Added generate balancedtree command to generate balanced trees
• Added reroot midpoint and reroot outgroup commands

v0.1.5

• New command to collapse lowly supported branches
• New command to compute total branch lengths
• New command to clear lengths and supports
• New commands to generate random trees
• New command to reroot a tree using an outgroup
• Command "compare edge" can take a multi tree newick file as input
• Command "shuffletips" can take a multi tree newick file as input
• Bug fixes:
  • Corrected deletion of tip when connected to multifurcated node
  • Corrected computation of median support

v0.1.4

• Modified EdgeIndex to use a more generic hashmap
• Added the command compute edgetrees to export multifurcating trees corresponding to each edges
• Added the possibility to have several trees as input of the prune command
• Added an option to print transfer/mast distance between input tree edges and compared tree in the compare edgescommand
• Added explanations for the help of command collapse brlen
• Added pvalues attached to edges of the trees (for support)
• Added an option for filtering branches in roccurve command
• Added a preliminary and greedy quartet enumeration
• Bug fixes:
  • Corrected the command line options for generate binarytree
  • Newick Parser: Now allow a length :<length> at the root node

v0.1.3

• Created README.md
• Modified compare command to use edge index
• Added compare edges command to list edges that are also found in another tree
• Bug fixes :
  • Corrected classical support computation
  • Corrected nb thread option in root command
  • Corrected boolean print in compare command

v0.1.2

• Added randlength command, to set branch lengths randomly (exponential distribution)
• Added compute consensus command, to compute the consensus of several trees. Branch lengths of the consensus are average branch lengths, and supports are percentage of trees in which the branch is found.

v0.1.1

v0.1.1

v0.1.0

First Version