- you can use conda  or pip and the requirements.txt file, 
example commands to do that are in requirements.txt

- alternatively, just run and see...its only a few, 
so errors will tell you whats missing
e.g. for python you need Biopython and pygenomeviz
e.g. you need the blast command line tools



# names of stuff #

- species/organisms are given simple names like {number}org
e.g., 1org as are there respective chromosomes/scaffolds/contigs
like {number}orgchr{number}, e.g. 1orgchr1. this is to avoid
format issues for the downstream program. 
the correspondence of these names with the actual species names 
is given in utils/mapping. this file is also used to construct 
a python dictionary in multiple scripts which can also be used
to see the correspondence (see e.g. custom/draw_synteny.py).
furthermore, there is a script "replace_name" in utils/ which
will take a txt file as the first argument and replace all
occurences of the fake names with the original names and write
it to a file whose name/path should be given as the second
argument


# workflow #

- look at the tutorial at https://anchored.bioinf.uni-leipzig.de/ 
for examples of a workflow with some of the most stable and 
hopefully most useful parts of AncST. this is mostly in out/stable

- in out/utils there are some...utils
- in out/gff you can find anchors and alignments in gff3 format
- in out/scaffolder you find an automated pipeline to scaffold 
genomes based on homology to closely related species as described 
in https://www.biorxiv.org/content/10.1101/2025.04.28.650980v2

- in out/experimental there are additional programs which are 
have been used successfully internally but are probably buggy 
and not general enough for most data sets to work out of the 
box at this point (feel free to contact karl.kaether@posteo.de 
to get help if you think one of those programs could benefit 
your analysis)
