A few functions for working with alignments in FASTA format
Requires Julia version >= 1.3.1
Julialign uses a slightly modified version of the bit-level coding scheme for nucleotides by Emmanuel Paradis (described here, and implemented in the R package ape).
| run | description |
|---|---|
| src/bootstrap.jl | Bootstrap an alignment by sampling sites with replacement |
| src/closest.jl | Find the closest sequence to a query by raw-distance |
| src/collapse.jl | Heuristic for stripping out the redundancy from a set of similar sequences |
| src/del_typer.jl | Type alignments for pre-specified deletions |
| src/pairsnp.jl | Get pairwise SNP distances within/between alignments |
For example, issue
julia src/collapse.jl -i input.fasta -r reference.fasta at the command line to run the collapse function.
Run any function with the -h flag to get a full list of options, e.g. julia src/bootsrap.jl -h
Be aware that command line options are subject to change at the moment.