Repository with all scripts used by Freitas & Nery (2022).
- 0-VectorBaseOrthologous.R was used to retrieve 1:1 orthologous gene families to perform the divergence time estimation for 19 Anopheles species and Aedes aegypti;
- After download transcripts for all species from VectorBase, 1-OrthologousToDNA.py was used to filter a single transcript for genes with multiple transcripts;
- 2-LoopPrank.py was used to align each gene;
- 3-LoopIQTREE.py was used to reconstruct a gene tree for each gene;
- Then SortaDate was used to select the 50 most clock-like genes to be used by MCMCtree to perfom the divergence time estimation.
- 4-RemoveStopCodon.py was used to remove possible stop codons in all 824 salivary gland proteins from Arcà et al. (2017);
- 5-DNAtoPTN.py was used to translate DNA seqs to aminoacid sequences;
- 6-SplitSequencesBySpecies.py was used to split all salivary gland protein sequences by species;
- 7-GetDNAfromOrthologous.py was used to create orthologous files with DNA sequence from OrthoFinder results.
- After align all sequences using 2-LoopPrank.py, 8-LoopGARD.py was used to run GARD;
- 9-LoopMEME.py was used to run MEME;
- 10-LoopFUBAR.py was used to run FUBAR;
- 11-HyPhy_results.R was used to retrieve all results from GARD, MEME and FUBAR.