Files

• Changes
• INSTALL
• LICENSE
• MANIFEST
• MANIFEST.SKIP
• META.yml
• Makefile.PL
• README
• bin/ali2fasta.pl
• bin/ali2phylip.pl
• bin/app-len-ids-ali.pl
• bin/change-ids-ali.pl
• bin/classify-ali.pl
• bin/export-itol.pl
• bin/extract-ali.pl
• bin/fasta2ali.pl
• bin/fetch-tax.pl
• bin/format-tree.pl
• bin/idealize-ali.pl
• bin/import-itol.pl
• bin/inst-abbr-ids.pl
• bin/inst-qual-filter.pl
• bin/inst-split-seqs.pl
• bin/inst-tax-filter.pl
• bin/jack-ali-dir.pl
• bin/list2mapper.pl
• bin/mask-ali.pl
• bin/phylip2ali.pl
• bin/prune-ali.pl
• bin/prune-tree.pl
• bin/rest-ids-ali.pl
• bin/setup-taxdir.pl
• bin/split-matrix.pl
• bin/split-rates-ali.pl
• bin/stock2ali.pl
• bin/subs-forest.pl
• bin/tab2mapper.pl
• bin/tax-filter-ali.pl
• bin/tax-mask-ali.pl
• bin/tree2list.pl
• bin/tree2tpl.pl
• bin/tseq2ali.pl
• lib/Bio/MUST/Core.pm
• lib/Bio/MUST/Core/Ali.pm
• lib/Bio/MUST/Core/Ali/Stash.pm
• lib/Bio/MUST/Core/Ali/Temporary.pm
• lib/Bio/MUST/Core/Constants.pm
• lib/Bio/MUST/Core/GeneticCode.pm
• lib/Bio/MUST/Core/GeneticCode/Factory.pm
• lib/Bio/MUST/Core/IdList.pm
• lib/Bio/MUST/Core/IdMapper.pm
• lib/Bio/MUST/Core/PostPred.pm
• lib/Bio/MUST/Core/PostPred/Composition.pm
• lib/Bio/MUST/Core/Roles/Aliable.pm
• lib/Bio/MUST/Core/Roles/Commentable.pm
• lib/Bio/MUST/Core/Roles/Filterable.pm
• lib/Bio/MUST/Core/Roles/Listable.pm
• lib/Bio/MUST/Core/Roles/Taxable.pm
• lib/Bio/MUST/Core/Seq.pm
• lib/Bio/MUST/Core/SeqId.pm
• lib/Bio/MUST/Core/SeqId/Filter.pm
• lib/Bio/MUST/Core/SeqMask.pm
• lib/Bio/MUST/Core/SeqMask/Freqs.pm
• lib/Bio/MUST/Core/SeqMask/Pmsf.pm
• lib/Bio/MUST/Core/SeqMask/Profiles.pm
• lib/Bio/MUST/Core/SeqMask/Rates.pm
• lib/Bio/MUST/Core/Taxonomy.pm
• lib/Bio/MUST/Core/Taxonomy/Category.pm
• lib/Bio/MUST/Core/Taxonomy/Classifier.pm
• lib/Bio/MUST/Core/Taxonomy/ColorScheme.pm
• lib/Bio/MUST/Core/Taxonomy/Criterion.pm
• lib/Bio/MUST/Core/Taxonomy/Filter.pm
• lib/Bio/MUST/Core/Taxonomy/Labeler.pm
• lib/Bio/MUST/Core/Taxonomy/MooseNCBI.pm
• lib/Bio/MUST/Core/Tree.pm
• lib/Bio/MUST/Core/Tree/Forest.pm
• lib/Bio/MUST/Core/Tree/Splits.pm
• lib/Bio/MUST/Core/Types.pm
• lib/Bio/MUST/Core/Utils.pm
• lib/Bio/MUST/Core/legacy.vim
• t/ali.t
• t/author-critic.t
• t/author-pod-syntax.t
• t/author-portability.t
• t/composition.t
• t/forest.t
• t/genetic_code.t
• t/id_list.t
• t/id_mapper.t
• t/moose_ncbi.t
• t/pmsf.t
• t/profiles.t
• t/rates.t
• t/seq.t
• t/seq_id.t
• t/seq_mask.t
• t/splits.t
• t/stash.t
• t/taxonomy.t
• t/temporary.t
• t/tree.t
• t/utils.t
• test-cat/ATP6_AA.fasta
• test-cat/ATP6_NT.fasta
• test-cat/ATP8_AA.fasta
• test-cat/ATP8_NT.fasta
• test-cat/COX1_AA.fasta
• test-cat/COX1_NT-a2p.ali
• test-cat/COX1_NT-a2p.fasta
• test-cat/COX1_NT.fasta
• test-cat/COX2_AA.fasta
• test-cat/COX2_NT.fasta
• test-cat/COX3_AA.fasta
• test-cat/COX3_NT.fasta
• test-cat/CYTB_AA.fasta
• test-cat/CYTB_NT.fasta
• test-cat/ND1_AA.fasta
• test-cat/ND1_NT.fasta
• test-cat/ND2_AA.fasta
• test-cat/ND2_NT.fasta
• test-cat/ND3_AA.fasta
• test-cat/ND3_NT.fasta
• test-cat/ND4L_AA.fasta
• test-cat/ND4L_NT.fasta
• test-cat/ND4_AA.fasta
• test-cat/ND4_NT.fasta
• test-cat/ND5_AA.fasta
• test-cat/ND5_NT.fasta
• test-cat/ND6_AA.fasta
• test-cat/ND6_NT.fasta
• test-mono/uce-996.nexus-must.idl
• test-mono/uce-996.nexus-must.tre
• test-poly/uce-99.nexus-must.idl
• test-poly/uce-99.nexus-must.tre
• test-poly/uce-990.nexus-must.idl
• test-poly/uce-990.nexus-must.tre
• test-poly/uce-993.nexus-must.idl
• test-poly/uce-993.nexus-must.tre
• test-poly/uce-994.nexus-must.idl
• test-poly/uce-994.nexus-must.tre
• test-poly/uce-995.nexus-must.idl
• test-poly/uce-995.nexus-must.tre
• test-poly/uce-997.nexus-must.idl
• test-poly/uce-997.nexus-must.tre
• test-poly/uce-998.nexus-must.idl
• test-poly/uce-998.nexus-must.tre
• test-poly/uce-999.nexus-must.idl
• test-poly/uce-999.nexus-must.tre
• test-sel/all_Terrabacteria_bac120_GCA.gtdb_tax
• test-sel/all_Terrabacteria_bac120_GCA.ncbi_tax
• test-sel/all_Terrabacteria_bac120_GCA.txt
• test-sel/all_Terrabacteria_bac120_metadata.gtdb_tax
• test-sel/all_Terrabacteria_bac120_metadata.idl
• test-sel/all_Terrabacteria_bac120_metadata.ncbi_tax
• test-sel/all_Terrabacteria_bac120_metadata.tsv
• test/AhHMA4.acc
• test/AhHMA4.ali
• test/AhHMA4.bb
• test/AhHMA4.bit
• test/AhHMA4_5.idl
• test/AhHMA4_5.lis
• test/AhHMA4_5_col_sep.idl
• test/AhHMA4_5_filtered.ali
• test/AhHMA4_5_reordered.ali
• test/AhHMA4_clustalw.ali
• test/AhHMA4_clustalw.fasta
• test/AhHMA4_clustalw_uni.ali
• test/AhHMA4_mapper.ali
• test/AhHMA4_mapper.alt
• test/AhHMA4_mapper.idm
• test/FTSW.tpl
• test/FTSW.tre
• test/G12210-O-S-1-NO.data
• test/G12210-O-S-1-NO.out
• test/G12210-O-S-1-NO.ref-tre
• test/G12210-O-S-1-NO.tre
• test/GNTPAN19392.ali
• test/GNTPAN19590.ali
• test/GNTPAN19593.ali
• test/GNTPAN19618.ali
• test/GNTPAN19639.ali
• test/GNTPAN19649.ali
• test/HMA234-euka-bor.ali
• test/HMA234-euka.ali
• test/HMA234-euka.bor
• test/HMA234-euka.una
• test/OG0000464-edit-MMETSP172-clade.txt
• test/OG0000464-edit-MMETSP172-collapse.txt
• test/OG0000464-edit-MMETSP172-color.txt
• test/OG0000464-edit-MMETSP172-label.txt
• test/OG0000464-edit-MMETSP172-range.txt
• test/OG0000464-edit-MMETSP172.idm
• test/OG0000464-edit-MMETSP172.tre
• test/OG0001014.fasta
• test/P-rpoB-CYANO10254.idm
• test/PBP3-clade.txt
• test/PBP3-collapse.txt
• test/PBP3-color.txt
• test/PBP3-label.txt
• test/PBP3-range.txt
• test/PBP3.arb
• test/PBP3.idl
• test/PBP3.tre
• test/PBP3_auto.tre
• test/PBP3_auto_phylum.nex
• test/PBP3_family.tre
• test/PBP3_family_phylum.nex
• test/PBP3_phylum_4color.nex
• test/ali_with_qm.ali
• test/ali_with_qm_temp.fasta
• test/ali_with_qm_temp_gaps.fasta
• test/archaea-mcr-concat-rootA.tre
• test/archaea-mcr-concat-rootB.tre
• test/archaea-mcr-concat.tre
• test/bacteria.cls
• test/bacteria.tax
• test/bacteria.taxids
• test/blocks-masked.ali
• test/blocks.ali
• test/blocks.blocks
• test/bmge.fasta
• test/bmge_loose.fasta
• test/bmge_medium.fasta
• test/bmge_strict.fasta
• test/cbs.ali
• test/cbs.fasta
• test/cbs.stockholm
• test/classifier-simple.idl
• test/classifier-zero.yaml
• test/classifier.yaml
• test/collapse.nex
• test/collapse.tre
• test/colors-itol-euka.txt
• test/complete.ali
• test/complete.fasta
• test/consense.out
• test/cyano.org-idm
• test/cyanos.arb
• test/cyanos_taxa.tre
• test/empty_seqs.ali
• test/euka-adl.cls
• test/fake-rootA.tre
• test/fake-rootAB.tre
• test/fake-rootB.tre
• test/fake-rootC.tre
• test/fake-rootCD.tre
• test/fake-rootD.tre
• test/fake-rootE.tre
• test/fake-rootEF.tre
• test/fake-rootF.tpl
• test/fake-rootF.tre
• test/fake-unroot.tpl
• test/fake-unroot.tre
• test/fetch-tax-baseid.idl
• test/fetch-tax-baseid.tax
• test/fetch-tax-gi-acc.idl
• test/fetch-tax-gi-acc.tax
• test/fetch-tax-gi.idl
• test/fetch-tax-gi.tax
• test/fetch-tax-mustid.idl
• test/fetch-tax-mustid.tax
• test/fetch-tax-name.idl
• test/fetch-tax-name.tax
• test/fetch-tax-taxid.idl
• test/fetch-tax-taxid.tax
• test/filter.fasta
• test/filter_tax.idm
• test/filter_tax_acc.idm
• test/filters.idl
• test/for-ppred-comp.phy
• test/for-ppred-prof.phy
• test/forest
• test/forest-ids
• test/forest.idm
• test/gapify.ali
• test/gapify_X.ali
• test/gapify_X.fasta
• test/gapify_gap.ali
• test/gapify_gap.fasta
• test/gb_loose.fasta
• test/gb_medium.fasta
• test/gb_strict.fasta
• test/gb_strict.phy_phyml_tree.arb
• test/gblocks.fasta
• test/gblocks_const.ali
• test/gblocks_gaps.fasta
• test/gblocks_masked.ali
• test/get_gtdb_taxonomy_from_gca.test
• test/get_ncbi_taxonomy_from_gca.test
• test/get_taxid_from_legacy_seq_id.test
• test/get_taxid_from_seq_id.test
• test/gi_mapper.fasta
• test/gi_mapper.idm
• test/insplit.fasta
• test/leaf_4_fra_bact.list
• test/lhc-prasino.splits.nex
• test/life.cls
• test/life_html.cls
• test/lifemrch.fra
• test/long-leaf-seqs.idl
• test/long-leaf-tree.tre
• test/map_coords.ali
• test/mask.ali
• test/misleading.idl
• test/mullidae-unrooted.tpl
• test/mullidae-unrooted.tre
• test/mullidae-well-rooted.tre
• test/neglist-out.ali
• test/neglist.ali
• test/neglist.idl
• test/new_seqs.ali
• test/nuclideal.ali
• test/nuclideal_0.25.ali
• test/nuclideal_0.5.ali
• test/nuclideal_1.ali
• test/nuclideal_2.ali
• test/obs-ppred-freqs-glb.tsv
• test/obs-ppred-freqs-reorder.tsv
• test/obs-ppred-freqs.tsv
• test/obs.idl
• test/outsplit.fasta
• test/parsimony.msk
• test/phylip-lr.phy
• test/phylip-rep.phy
• test/phylip.ali
• test/phylip.fasta
• test/phylip.p80
• test/phylip.phy
• test/plantae.arb
• test/plantae_ali.arb
• test/ppred-1.phy
• test/ppred-10.phy
• test/ppred-11.phy
• test/ppred-12.phy
• test/ppred-13.phy
• test/ppred-14.phy
• test/ppred-15.phy
• test/ppred-16.phy
• test/ppred-17.phy
• test/ppred-18.phy
• test/ppred-19.phy
• test/ppred-2.phy
• test/ppred-20.phy
• test/ppred-21.phy
• test/ppred-22.phy
• test/ppred-23.phy
• test/ppred-24.phy
• test/ppred-25.phy
• test/ppred-26.phy
• test/ppred-27.phy
• test/ppred-28.phy
• test/ppred-29.phy
• test/ppred-3.phy
• test/ppred-30.phy
• test/ppred-31.phy
• test/ppred-32.phy
• test/ppred-33.phy
• test/ppred-34.phy
• test/ppred-35.phy
• test/ppred-36.phy
• test/ppred-37.phy
• test/ppred-38.phy
• test/ppred-39.phy
• test/ppred-4.phy
• test/ppred-40.phy
• test/ppred-41.phy
• test/ppred-42.phy
• test/ppred-43.phy
• test/ppred-44.phy
• test/ppred-45.phy
• test/ppred-46.phy
• test/ppred-47.phy
• test/ppred-48.phy
• test/ppred-49.phy
• test/ppred-5.phy
• test/ppred-50.phy
• test/ppred-6.phy
• test/ppred-7.phy
• test/ppred-8.phy
• test/ppred-9.phy
• test/ppred-freqs-by-seq.tsv
• test/primate.fas
• test/primate.nex
• test/primate.rates
• test/protideal.ali
• test/protideal_0.25.ali
• test/protideal_0.5.ali
• test/protideal_1.ali
• test/protideal_2.ali
• test/recode_seqs.ali
• test/rg-supermatrix-IQTREE.rate
• test/root_tree_names_rooted_ladder.tre
• test/root_tree_names_rooted_ladder_hand.tre
• test/root_tree_names_unrooted.tre
• test/rooted-bp.grp
• test/rooted-bp.nbs
• test/rooted-bp.tre
• test/rooted-pp.grp
• test/rooted-pp.nbs
• test/rooted-pp.tre
• test/secure.ali
• test/selection.idl
• test/selection.tax
• test/seqid-grp-nbs.grp
• test/seqid-grp-nbs.tre
• test/seqs4uc.ali
• test/shortlist.clo.idm
• test/shortlist.clo.phy_phyml_tree.txt
• test/shortlist.clo.tre
• test/sim.idl
• test/simple.tre
• test/sparse_seqs.ali
• test/sparse_seqs.fasta
• test/sparse_seqs_pad.ali
• test/sparse_seqs_pad.fasta
• test/speclist.idm
• test/stash.fasta
• test/store-una-blocks-align.blocks
• test/store-una-ex-seq.ali
• test/store-una.una
• test/store_blocks.blocks
• test/superideal.ali
• test/superideal_0.1.ali
• test/superideal_0.3.ali
• test/superideal_0.5.ali
• test/superideal_0.7.ali
• test/superideal_0.9.ali
• test/supermatrix-CATG-A-sample.rate
• test/supermatrix-CATG-B-sample.rate
• test/supermatrix-a2p.ali
• test/supermatrix-bin0.ali
• test/supermatrix-bin1.ali
• test/supermatrix-bin2.ali
• test/supermatrix-bin3.ali
• test/supermatrix-bin4.ali
• test/supermatrix-bin5.ali
• test/supermatrix-bin6.ali
• test/supermatrix-bin7.ali
• test/supermatrix-bin8.ali
• test/supermatrix-bin9.ali
• test/supermatrix-noconstant.msk
• test/supermatrix-noconstant.phy
• test/supermatrix.ali
• test/supermatrix.phy
• test/tab_mapper_gi2taxid.idm
• test/tab_mapper_mustids.idm
• test/tab_mapper_mustids.tsv
• test/tab_mapper_with_idm.idm
• test/tab_mapper_with_idm.tsv
• test/tax-fake-rootA.tre
• test/tax-fake-rootAB.tre
• test/tax-fake-rootB.tre
• test/tax-fake-rootC.tre
• test/tax-fake-rootCD.tre
• test/tax-fake-rootD.tre
• test/tax-fake-rootE.tre
• test/tax-fake-rootEF.tre
• test/tax-fake-rootF.tre
• test/taxmask.ali
• test/taxmask.yaml
• test/taxmask_metazoans.fasta
• test/taxmask_opisthokonts.fasta
• test/temp.fasta
• test/temp_degap.fasta
• test/temp_degap_nowrap.fasta
• test/temp_prefix.fasta
• test/test-delta.rates
• test/test-othr.meansiterates
• test/test-pmsf-archaea.sitefreq
• test/test-pmsf-chi-square.stats
• test/test-pmsf-euka.sitefreq
• test/test-pmsf.ali
• test/test-self.meansiterates
• test/test_recode_expected.ali
• test/test_uc_expected.ali
• test/thermus.fas
• test/thermus.nex
• test/thermus.rates
• test/tinyseq.xml
• test/tinyseq_ks0.ali
• test/tinyseq_ks1.ali
• test/tricky.names
• test/tricky.tax
• test/uc_seqs.ali
• test/unaligned.ali
• test/underscores.idm
• test/uniq.ali
• test/unrooted-bp.grp
• test/unrooted-bp.nbs
• test/unrooted-bp.tre
• test/unrooted-pp.grp
• test/unrooted-pp.nbs
• test/unrooted-pp.tre
• test/upsk.ali
• test/upsk.stockholm