brocode

Collection of scripts made by yours truly. Main usage will be as versioning system and repository.

Name		Name	Last commit message	Last commit date
Latest commit History 60 Commits
Phylogeny/Tree		Phylogeny/Tree
matters_arising		matters_arising
nee_matters_arising		nee_matters_arising
pbamp		pbamp
treeColors		treeColors
#beskow_phylobayes_convergence.sh#		#beskow_phylobayes_convergence.sh#
#uppmax_phylobayes_convergence.sh#		#uppmax_phylobayes_convergence.sh#
NexusTreeAddColors.pl		NexusTreeAddColors.pl
README.md		README.md
aa_recoding.pl		aa_recoding.pl
add_intergenic_space_features.py		add_intergenic_space_features.py
add_intron_features.py		add_intron_features.py
add_orfs_to_intergenic_regions.py		add_orfs_to_intergenic_regions.py
add_orfs_to_intergenic_regions_blasto.py		add_orfs_to_intergenic_regions_blasto.py
alignment_pruner.pl		alignment_pruner.pl
all2many.pl		all2many.pl
assign-contigs2domains.pl		assign-contigs2domains.pl
assign-genes2domains.pl		assign-genes2domains.pl
beskow_phylobayes.sh		beskow_phylobayes.sh
beskow_phylobayes_convergence.sh		beskow_phylobayes_convergence.sh
beskow_phylobayes_ppred.sh		beskow_phylobayes_ppred.sh
beskow_submit_phylobayes.sh		beskow_submit_phylobayes.sh
beskow_submit_phylobayes_convergence.sh		beskow_submit_phylobayes_convergence.sh
beskow_submit_phylobayes_ppred.sh		beskow_submit_phylobayes_ppred.sh
broCode.code-workspace		broCode.code-workspace
calcCARSC.py		calcCARSC.py
calcNARSC.py		calcNARSC.py
clusters2faa.pl		clusters2faa.pl
clusters2matrix.pl		clusters2matrix.pl
colorFastq.pl		colorFastq.pl
compare_assemblies.py		compare_assemblies.py
concatenateRenameAlignment.pl		concatenateRenameAlignment.pl
countTaxaInCluster.pl		countTaxaInCluster.pl
countTaxaPerOG_eggNOG.pl		countTaxaPerOG_eggNOG.pl
count_tripartitions.py		count_tripartitions.py
doColorTree.sh		doColorTree.sh
doConcatRaxml.sh		doConcatRaxml.sh
doIqtreeTopologyTest.pl		doIqtreeTopologyTest.pl
doSelectTreeTaxa.sh		doSelectTreeTaxa.sh
doStandardRaxml.sh		doStandardRaxml.sh
doUpdateOGs.sh		doUpdateOGs.sh
drawChiSquarePlot.R		drawChiSquarePlot.R
drawChiSquarePlot.sh		drawChiSquarePlot.sh
drawCompositionPCA.R		drawCompositionPCA.R
drawCompositionPCA.sh		drawCompositionPCA.sh
extractBlastTab.pl		extractBlastTab.pl
fasta2taxo_complete4.pl		fasta2taxo_complete4.pl
fastaNamesSizes.pl		fastaNamesSizes.pl
figtree_block		figtree_block
filterAssemblyLengthCov.pl		filterAssemblyLengthCov.pl
filterFastaFromLength.pl		filterFastaFromLength.pl
fix_genes_with_false_introns.py		fix_genes_with_false_introns.py
getAcc.pl		getAcc.pl
getCodingDensity.pl		getCodingDensity.pl
getCompleteness.sh		getCompleteness.sh
getGCcontent.pl		getGCcontent.pl
getIntergenicSpace.pl		getIntergenicSpace.pl
getRecords.pl		getRecords.pl
getSsuLsuDistance.pl		getSsuLsuDistance.pl
get_CDSs.pl		get_CDSs.pl
get_GI_loc.pl		get_GI_loc.pl
get_gf2cog2arcogs_mapping.py		get_gf2cog2arcogs_mapping.py
get_rRNAs.pl		get_rRNAs.pl
gff2fasta.pl		gff2fasta.pl
hideSupportValues.pl		hideSupportValues.pl
meganpaths2contigdomaincount.pl		meganpaths2contigdomaincount.pl
monitorRunningJob.R		monitorRunningJob.R
newick2Nexus.pl		newick2Nexus.pl
parseSAMHappyPairs.pl		parseSAMHappyPairs.pl
parseSplitcounts.pl		parseSplitcounts.pl
parse_tripartition_counts.py		parse_tripartition_counts.py
perun_blast.sh		perun_blast.sh
perun_iqtree.sh		perun_iqtree.sh
perun_prep_supermatrix.sh		perun_prep_supermatrix.sh
pickLongestFromIdenticals.pl		pickLongestFromIdenticals.pl
plot_pb_stats.R		plot_pb_stats.R
plot_pb_stats.old.R		plot_pb_stats.old.R
plot_relative_intron_locations.py		plot_relative_intron_locations.py
prepSupermatrix.sh		prepSupermatrix.sh
prepSupermatrix.sh~		prepSupermatrix.sh~
purge_false_introns.py		purge_false_introns.py
reduceRedundancy.sh		reduceRedundancy.sh
removeIdenticalSequences.pl		removeIdenticalSequences.pl
remove_species_in_splitSet.pl		remove_species_in_splitSet.pl
renameContigs.pl		renameContigs.pl
render_tree.py		render_tree.py
replaceSeqsWithRandomSeqs.pl		replaceSeqsWithRandomSeqs.pl
selectSequences.pl		selectSequences.pl
sequenceCutter.pl		sequenceCutter.pl
showColumns.sh		showColumns.sh
sort_gff3.py		sort_gff3.py
splice_region.py		splice_region.py
splitMultiFasta.pl		splitMultiFasta.pl
ssuPhylogeny.sh		ssuPhylogeny.sh
summarize.sh		summarize.sh
taxaColorsSort.list		taxaColorsSort.list
taxaColorsSort_Alphas.txt		taxaColorsSort_Alphas.txt
tegner_spades.sh		tegner_spades.sh
tegner_submit_spades.sh		tegner_submit_spades.sh
test		test

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