Gaius-Augustus/Augustus v3.4.0

3.4.0

on GitHub

List of changes from version 3.3.3 to 3.4.0 (until Dec 11th, 2020)
- enable making of a Debian package that includes the CGP functionality
- shortrunning (make test) and longrunning tests for monitoring functionality and performance
- drop dependency on static bam library, e.g. of bam2wig
- new program pp_simScore to score a protein against a protein profile (.prfl)
- new option --/CompPred/printExonCandsMSA=1 for CGP to produce MSAs of candidate coding regions
- new scripts augustify, fix_in_frame_stop_codon_genes.py
- new default: softmasking is assumed
- compile with CGP and ZIPINPUT support by default
- compile with SQLite and MySQL support for CGP (switch of by adding SQLite = false and MySQL = false to common.mk)
- new species Cassiopea xamachana, Ptychodera flava, Argopecten irridians, Nemopilema nomurai
Notospermus_geniculatus, Chrysaora chesapeakeij, Ectocarpus siliculosus, Trichoplax adhaerens,
Aurelia aurita, Rhopilema esculentum, Encephalitozoon cuniculi, Gonapodya prolifera, Dunaliella_salina
Sordaria macrospora, Sphaceloma murrayae, Vitrella brassicaformis, Monoraphidium neglectum, Raphidocelis subcapita,
Ostreococcus tauri, Ostreococcus sp. lucimarinus, Micromonas pusilla, Micromonas_commoda, Chlamydomonas eustigma,
Thalassiosira pseudonana, Pseudo-nitzschia multistriata, Phaeodactylum tricornutum, Fragilariopsis cylindrus,
Fistulifera solaris, Bathycoccus prasinos, Chloropicon primus
- added Windows Subsystem for Linux Installation documentation
- fixes of bugs, compiler warnings