User's Guide for version 3
Available formats:
Table of Contents
- Introduction
- Installation
- Running the program
- Input
- Output
- Substitution models
- Insertion/deletion models
- Models and Priors
- Partitioned data sets
- Ancestral sequence reconstruction
- Convergence and Mixing: Is it done yet?
- Alignment utilities
- Tree utilities
- Compiling BAli-Phy
- Frequently Asked Questions (FAQ)
Manual pages
Manual pages for tools
- alignment-cat
- alignment-chop-internal
- alignment-consensus
- alignment-distances
- alignment-draw
- alignment-find
- alignment-gild
- alignment-indices
- alignment-info
- alignment-max
- alignments-diff
- alignment-thin
- alignment-translate
- cut-range
- draw-tree
- mctree-mean-lengths
- model_P
- pickout
- statreport
- stats-cat
- bali-subsample
- tree-mean-lengths
- tree-partitions
- trees-bootstrap
- trees-consensus
- trees-distances
- trees-to-SRQ
- tree-tool