Files in HajkD/orthologr

Comparative Genomics with R

.Rbuildignore

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.travis.yml

COPYING

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/DivergenceMap.R R/OF2CoreOrthologs.R R/OF2Orthologs.R R/RcppExports.R R/base.R R/blast.R R/blast_best.R R/blast_rec.R R/check_annotation.R R/check_ram.R R/clean_all_folders.R R/codon_aln.R R/compute_dnds.R R/dNdS.R R/diamond.R R/diamond_best.R R/diamond_rec.R R/divergence_stratigraphy.R R/extract_features.R R/filter_best_hit.R R/filter_core_set.R R/filter_core_set_lnc.R R/filter_dNdS.R R/generate_ortholog_tables.R R/generate_ortholog_tables_all.R R/gestimator.R R/get_filename.R R/import_ortholog_tables_all.R R/io.R R/is_installed_blast.R R/is_installed_clustalo.R R/is_installed_diamond.R R/is_installed_kaks_calculator.R R/is_installed_mafft.R R/is_installed_muscle.R R/is_installed_orthofinder.R R/is_installed_tcoffee.R R/is_istalled_clustalw.R R/lnc_map_core_orthologs.R R/lnc_map_counts.R R/map.generator.R R/map.generator.lnc.R R/multi_aln.R R/orthofinder2.R R/orthologs.R R/orthologs.lnc.R R/orthologs_lnc.R R/pairwise_aln.R R/plot_diverse_homology_thresholds.R R/plot_diverse_homology_thresholds_core_orthologs.R R/plot_pairwise_orthologs.R R/promotor_divergence_estimation.R R/promotor_divergence_of_orthologous_genes.R R/read.dnds.tbl.R R/read.ortholog.table.R R/retrieve_core_orthologs.R R/retrieve_longest_isoforms.R R/retrieve_longest_isoforms_all.R R/select_orthologs.R R/set_blast.R R/set_diamond.R R/set_path.R R/substitutionrate.R R/testCoreOrthoParamsGeneLocus.R R/testCoreOrthoParamsSplicceVariant.R R/transl.R R/translate_cds_to_protein.R R/translate_cds_to_protein_all.R R/utils.R R/write.proteome.R R/ws_wrap.R README.md

Read-and-delete-me

docs/404.html

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docs/articles/Install.html

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docs/articles/divergence_stratigraphy.html

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docs/sitemap.xml

inst/CITATION

inst/KaKs_Calc_parser/parseFastaIntoAXT.pl

inst/REFERENCES.bib

inst/pal2nal/pal2nal.v14/README

inst/pal2nal/pal2nal.v14/for_paml/test.cnt

inst/pal2nal/pal2nal.v14/for_paml/test.codeml.ori

inst/pal2nal/pal2nal.v14/for_paml/test.tree

inst/pal2nal/pal2nal.v14/pal2nal.pl

inst/pal2nal/pal2nal.v14/test.aln

inst/pal2nal/pal2nal.v14/test.nuc

inst/seqs/aa_seqs.aln

inst/seqs/aa_seqs.dnd

inst/seqs/aa_seqs.fasta

inst/seqs/dna_seqs.fasta

inst/seqs/example.fa

inst/seqs/example_alyra_aa.faa

inst/seqs/example_athal_aa.faa

inst/seqs/example_brapa_aa.faa

inst/seqs/example_thalo_aa.faa

inst/seqs/map_gen_example/ortho_lyra_cds.fasta

inst/seqs/map_gen_example/ortho_thal_cds.fasta

inst/seqs/multi_aln_example.fasta

inst/seqs/ortho_lyra_aa.fasta

inst/seqs/ortho_lyra_cds.fasta

inst/seqs/ortho_lyra_cds_1000.fasta

inst/seqs/ortho_thal_aa.fasta

inst/seqs/ortho_thal_cds.fasta

inst/seqs/ortho_thal_cds_1000.fasta

inst/seqs/pal2nal.aln

inst/testcases/cause_multaln_error_query.fasta

inst/testcases/cause_multaln_error_subject.fasta

man/.DS_Store

man/blast.Rd man/blast_best.Rd man/blast_rec.Rd man/cds2aa.Rd man/check_annotation.Rd man/clean_all_folders.Rd man/codon_aln.Rd man/compute_dnds.Rd man/dNdS.Rd man/diamond.Rd man/diamond_best.Rd man/diamond_rec.Rd man/divergence_map.Rd man/divergence_stratigraphy.Rd man/extract_features.Rd

man/figures/logo.png

man/filter_best_hits.Rd man/filter_core_set.Rd man/filter_core_set_lnc.Rd man/filter_dNdS.Rd man/generate_ortholog_tables.Rd man/generate_ortholog_tables_all.Rd man/import_ortholog_tables_all.Rd man/lnc_map_core_orthologs.Rd man/lnc_map_counts.Rd man/map_generator_dnds.Rd man/map_generator_lnc.Rd man/multi_aln.Rd man/orthofinder2.Rd man/orthofinder2_retrieve_core_orthologs.Rd man/orthologs.Rd man/orthologs_lnc.Rd man/pairwise_aln.Rd man/plot_diverse_homology_thresholds.Rd man/plot_diverse_homology_thresholds_core_orthologs.Rd man/plot_pairwise_orthologs.Rd man/promotor_divergence_estimation.Rd man/promotor_divergence_of_orthologous_genes.Rd man/read.cds.Rd man/read.dnds.tbl.Rd man/read.genome.Rd man/read.proteome.Rd man/retrieve_core_orthologs.Rd man/retrieve_longest_isoforms.Rd man/retrieve_longest_isoforms_all.Rd man/select_orthologs.Rd man/set_blast.Rd man/set_diamond.Rd man/substitutionrate.Rd man/testCoreOrthoParamsGeneLocus.Rd man/testCoreOrthoParamsSpliceVariant.Rd man/transl.Rd man/translate_cds_to_protein.Rd man/translate_cds_to_protein_all.Rd man/write.proteome.Rd

orthologr-conda-env.sh

orthologr.Rproj

orthologr.yml

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src/.gitignore

src/Comeron95.h

src/Comparisons.h

src/Grantham.h

src/GranthamWeights.h

src/Kimura80.h

src/Makevars

src/RcppExports.cpp

src/RedundancyCom95.h

src/Sequence.h

src/SingleSub.h

src/Sites.h

src/ThreeSubs.h

src/TwoSubs.h

src/gestimator.cpp

src/orthologr_init.c

tests/testthat.R tests/testthat/test-blast.R tests/testthat/test-blast_best.R tests/testthat/test-blast_rec.R tests/testthat/test-cds2aa.R tests/testthat/test-codon_aln.R tests/testthat/test-dNdS.R tests/testthat/test-divergence_map.R tests/testthat/test-divergence_stratigraphy.R tests/testthat/test-extract_features.R tests/testthat/test-filter_best_hits.R tests/testthat/test-filter_dNdS.R tests/testthat/test-generate_ortholog_table.R tests/testthat/test-map_generator.R tests/testthat/test-map_generator_lnc.R tests/testthat/test-multi_aln.R tests/testthat/test-orthofinder2.R tests/testthat/test-orthofinder2_retrieve_core_orthologs.R tests/testthat/test-orthologs.R tests/testthat/test-orthologs_lnc.R tests/testthat/test-pairwise_aln.R tests/testthat/test-read.cds.R tests/testthat/test-read.dnds.tbl.R tests/testthat/test-read.genome.R tests/testthat/test-read.proteome.R tests/testthat/test-retrieve_longest_isoforms.R tests/testthat/test-select_orthologs.R tests/testthat/test-set_blast.R tests/testthat/test-substitutionrate.R tests/testthat/test-transl.R tests/testthat/test-translate_cds_to_protein.R vignettes/Install.Rmd vignettes/blast.Rmd vignettes/dNdS_estimation.Rmd vignettes/divergence_stratigraphy.Rmd vignettes/orthology_inference.Rmd vignettes/sequence_alignments.Rmd

HajkD/orthologr documentation built on Oct. 13, 2023, 12:11 a.m.