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200 Commits
00.scripts
00.scripts
 
 
01.dadi_fsc
01.dadi_fsc
 
 
02.manual_check_gene
02.manual_check_gene
 
 
03.treemix
03.treemix
 
 
04.saguarogw
04.saguarogw
 
 
05.beagleAndHWE
05.beagleAndHWE
 
 
06.smcpp
06.smcpp
 
 
07.chloroplast_assembly
07.chloroplast_assembly
 
 
08.stairway_plot
08.stairway_plot
 
 
09.psmc
09.psmc
 
 
10.ihs
10.ihs
 
 
11.samtools_callSNP
11.samtools_callSNP
 
 
12.mutation_number
12.mutation_number
 
 
15.GO_analysis
15.GO_analysis
 
 
16.maf2positive_selection
16.maf2positive_selection
 
 
17.gwas
17.gwas
 
 
18.maf_related_scripts
18.maf_related_scripts
 
 
19.kegg_analysis
19.kegg_analysis
 
 
20.pseudogene
20.pseudogene
 
 
22.ibd_analysis
22.ibd_analysis
 
 
24.transcriptome
24.transcriptome
 
 
25.inparanoid-ghostz
25.inparanoid-ghostz
 
 
26.kegg_enrichment
26.kegg_enrichment
 
 
27.fastEPRR
27.fastEPRR
 
 
28.phylogeny_reconstruction
28.phylogeny_reconstruction
 
 
29.pantherAnalysis
29.pantherAnalysis
 
 
30.divergence_time_mcmctree
30.divergence_time_mcmctree
 
 
31.gene_charactor_calculate
31.gene_charactor_calculate
 
 
32.mafExtractGene_keepGenesFromGff
32.mafExtractGene_keepGenesFromGff
 
 
33.merge_gff
33.merge_gff
 
 
34.hyphy
34.hyphy
 
 
35.novel_gene
35.novel_gene
 
 
36.reseq_pipeline
36.reseq_pipeline
 
 
37.ensembl_dat_extract
37.ensembl_dat_extract
 
 
38.reference_based_assembly/01.generate_reference
38.reference_based_assembly/01.generate_reference
 
 
39.housekeepingGeneList
39.housekeepingGeneList
 
 
40.tm_predictor
40.tm_predictor
 
 
41.kaks_calculator
41.kaks_calculator
 
 
42.prediction
42.prediction
 
 
43.differentially_expressed_genes
43.differentially_expressed_genes
 
 
44.reciprocal_best_hit
44.reciprocal_best_hit
 
 
.gitignore
.gitignore
 
 
LICENSE
LICENSE
 
 
README.md
README.md
 
 

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bio_tools (Useful bioinformatic scripts)

  • script for handling fasta file with or without bioperl
  • scripts for running dadi quickly

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Useful bioinformatic scripts

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MPL-2.0 license
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  • Shell 66.9%
  • Perl 28.0%
  • Forth 2.6%
  • Python 2.2%
  • Smarty 0.2%
  • Rebol 0.1%