# This file was automatically generated by Dist::Zilla::Plugin::Manifest v6.017.
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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/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
instant/inst-abbr-ids.pl
instant/inst-qual-filter.pl
instant/inst-split-seqs.pl
instant/inst-tax-filter.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/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/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/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/stash.t
t/taxonomy.t
t/temporary.t
t/tree.t
t/utils.t
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/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/cyano.org-idm
test/cyanos.arb
test/cyanos_taxa.tre
test/empty_seqs.ali
test/euka-adl.cls
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_taxid_from_legacy_seq_id.test
test/get_taxid_from_seq_id.test
test/get_taxonomy_from_gca.test
test/gi_mapper.fasta
test/gi_mapper.idm
test/insplit.fasta
test/leaf_4_fra_bact.list
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/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/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/taxdump/gc.prt
test/taxdump/misleading.dmp.unused
test/taxdump/names_u1.dmp.unused
test/taxdump/nodes_u1.dmp.unused
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/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