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
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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