- here are some util scripts and meta data (further described below) and the anchors in python pickles with verbose info ("anchors") and succinct info ("compressed_maps_multis_to_one")

- phylogeny: based on the anchor alignments, a UPGMA and NJ tree was calculated and is available here. produced by ../scripts_which_produced_these_results/phylogeny_from_anchors.py
- convert_ncbi_idents.py can be used to convert ncbi accessions back to names like "python3 convert_ncbi_idents.py NJTree.nwk NJTree.nwk_names"
- root_NJ_tree_at_midpoint.py can be used to root the NJ trees

1. put a protein or nucleotide sequence that you want to find orthologues for in a fasta file
2. put a list of all organisms to search for homologs in a file named "orgs". one organism per line
3. the genomes for the organisms in orgs have to be accessible in a path where they are named:
{name_which_is_in_orgs}.fasta
-> e.g.:

orgs:
dmel
human

genomes accessible somewhere:
dmel.fasta
human.fasta

3. make sure the clasp.x executable in this folder can actually be run. otherwise compile for your machine
see http://legacy.bioinf.uni-leipzig.de/Software/clasp/
5. run find_pot_homologs with protein.fasta/nucleotides.fasta as the first and the path to the genomes as the second argument
and specifiy as the third argument if its a protein (prot) or nucleotide (nucl) sequence
-> ./find_pot_homologs.py protein.fasta path/to/genomes/ prot

6. there will be a file coords in the root folder (.. from here) with the chained hits that can be used
for further analysis (e.g. in ../MCScanX or ../custom)

