Other tools

Other tools

dendrogram-from-matrix

Build the same trees and PCoA plot as genome-comparator from any square distance matrix.

dendrogram-from-matrix -i matrix.tsv -o out/ [--linkage average] [--nj] [--me] [--pcoa]
                       [--metadata metadata.tsv] [--color-by COLUMN]

• Input: .tsv, .csv, .xlsx or .xls. The first row and first column hold the sample names.
• The matrix must be square, symmetric, complete and non-negative. Rows and columns may be in any order.
• Output files are named after the input file, e.g. matrix_hc.nwk, matrix_PCoA.html.
• Bootstrap support is not available here, because it needs the genomes.

tree-collapser

Collapse clades whose average distance to their tips is smaller than a threshold. Useful to simplify large trees with many near-identical genomes.

tree-collapser -i tree.nwk -o collapsed.nwk -d 0.001

A collapsed clade is replaced by a single tip named <first tip> {<other tips>}. Bootstrap support values of the remaining clades are kept.

tree-renamer

Rename the tips of a tree using a two-column tab-separated table: current name, new name.

tree-renamer -i tree.nwk -o renamed.nwk -r rename.tsv

• Only exact matches are renamed: S1 never changes S10.
• Names from the table that are not found in the tree, and new names shared by several tips, are listed in warnings.
• Bootstrap support values are kept.