evigene23jul15.tar
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extract to evigene/ folder with command: tar -xf evigene23jul15.tar

EvidentialGene update 2023-jul-15 notes
 * Mostly updates to Gnodes portion (DNA measurements of genomes), including corrections with
   validation of long-read DNA measures.  
 * See Gnodes documents (2nd, 3rd in progress) at 
   http://arthropods.eugenes.org/EvidentialGene/other/gnodes/gnodesdoc/
   http://arthropods.eugenes.org/EvidentialGene/other/gnodes/gnodesdoc/gnodes23daphnmodels_doc/  (2nd or 3rd)

Additions
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    scripts/fagffmask.pl  : small tool to mask fasta from gff annots
    scripts/genes/  altparsnpdist.pl snp3aprecall.pl tr2dupgeneclass1a.pl : classify duplicated genes using DNA
      coverage-depth/copynum measures from Gnodes, applied to transcript assemblies.  Still in development.
    scripts/genoasm/ 
       asm_evd_filter.pl asmlink2refchr.pl : tools for chromosome assembly (DNA) to measure contig evidence for filtering
       and to link contigs to reference chromosome assembly
       gnodes_sam2covtab23jul.pl and gnodes_sam2genecov22jul.pl : updates for long-read DNA to gnodes
    scripts/genoasm/gnodes_work/
       run_tandreptfind2d.sh, run_kmc_readasmset4e.sh, run_kmc_crareduce4e.sh, kmc_dna_asm_copynum_corn.txt
       are scripts used for gnodesdoc/gnodes23daphnmodels_doc/ and may be added to Gnodes pipeline later. Used in
       measuring very high copynumber components of genomes (eg. Satellite DNA, duplicate genes, transposons).

    scripts/omcl/newickparse.pl : parse Newick tree structure
    scripts/rnaseq/asmrna_dupfilter4c.pl  : update to transcripts classifier of tr2aacds

Updated
-------------
   scripts/evgpipe_sra2genes.pl : sra2genes pipeline update (4v is same)
   scripts/genes/altparclassify.pl : update to altparclassify, used in tr2ncrna pipeline
   scripts/genoasm/gnodes_ pipe,annotate,covsum,sam2covtab,sam2genecov : various updates to Gnodes portions
   miscellaneous updates to 
     scripts/prot tr2aacds.pl traa2cds.pl cdsalignkaks.pl 
     scripts/genes/ blast2evgff.pl ncbigff2evg.pl trclass2pubset.pl
     scripts/makeblastscore.pl