New functionalities:

• Parsing confidence values when reading nextstrain format (--input-format nextstrain)
• Added Closest Tips information (from each node+tips) in gotree stats nodes (42685fa)
• Added tree pruning while keeping phylogenetic diversity gotree prune --random <x> --diversity (ad827fe, 40ae031)

Updates:

• Logo : Updated goalign/gotree logo
• GO: Updated go to version 1.24.11 (47f9aae, e576594)

• Added gotree brlen addcommand
• Modified gotree lttto take mutations or dates
• Added option gotree matrix --avg to compute average distance matrix
• Added option gotree mutations --eemto count emergences (as in https://doi.org/10.1093/gbe/evae040)
• Added option gotree comment clear --terminal to remove comments on terminal tips/branches only
• Corrected transfer index computation for equal min distance branches
• Added options gotree brlen setrand --min-len and --max-len
• Corrected Newick parsing (thanks @lucblassel ) 9f0bbcc
• Renamed gotree prune date to gotree cut date
• Added options gotree cut date --min-date and --max-date
• Corrected gotree reroot outgroup with a 0 length branch
• Added option gotree annotate --subtrees to annotate nodes and all their downstream nodes with some annotations
• Updated date parsing
• Added command goalign rtt generating root (and internal nodes) to tip data + plots
• Added option gotree resolve --rooted to output a rooted tree (root is randomly resolved).

• Corrected tindex computation (4fb145b)
• gotree matrix can take the option --metric to choose between branch length, bootstrap supports, or none 26ea287
• Added several metrics to compare trees (thanks @lucblassel ) 16bb1ae
• Added command gotree brlen set to set the length of all branches, and options --internal and --external a61803b
• Added command gotree compute mutations to extract the list of mutations along the branches of a phylogenetic tree, given the sequences of all internal and external nodes 76f7e3
• Updated newick parser to allow ';' in node/branch comments c7e2aa1
• Added command gotree collapse name to collapse branches that have a given name/id 0b9f8fa
• Added command gotree ltt to compute lineage through time data / plot (doc)

• Added support for Nextstrain json tree input with option --format nextstrain
• Update go to version 1.19

• Added option --annotation-fileto gotree draw command, to color tips (thanks @lucblassel #19 !)
• Updated tbe support to take into account equally distant branches in the output logs
• Added branch depth in tbe log
• Added command gotree comment transfer to transfer node names to comments
• Added parent/child node names in gotree stats nodesoutput
• Added comments compared edge comment to gotree compare edges
• Updated go to 1.18.3

• gotree stats tips now gives the length of the terminal branch + the root to tip length
• Added gotree resolve name command, that adds a new tip (with a 0-length branch) at each named internal node
• gotree stats edges now gives (for rooted trees) the number of branches from the root (output columns have changed)
• Minor corrections (comments, doc, etc.)
  From v0.4.3a:
• Added gotree graft command (doc)
• Added gotree collapse cladecommand (doc)
• Updated gotree prune command to take into account internal nodes with a single child

• Added gotree graft command (doc)
• Added gotree collapse cladecommand (doc)
• Updated gotree prune command to take into account internal nodes with a single child

• Corrected -i option for command labels
• Switched from dep to go modules
• Github actions
• Added --translateoption to reformat nexus (replaces tip names by indices, and prints a translation table in the output nexus format)
• Switched to go 1.16.4
• Solved some drawing problems (#15, partly)
• Updated citation

• Correction for rooted trees
• Changed goalign to v0.3.3c #8
• Added options --rm-quotes and --add-quotes to gotree rename #9
• Modified Parsimony / number of steps
• Addded --rf option to compare trees #10
• Added options --root and --tips to collapse brlength, support, and and depth commands #12
• Added labels command #13

• Added options --root and --tips to collapse brlength, support, and depth commands