29197f4e1b1721163f6ea9fe9fb17f11 *DESCRIPTION
1bc7dc2488b95ab865edef61f836ca03 *NAMESPACE
a714e88b36f244237d359f67b865b254 *NEWS.md
29f62ad0497a6ef0563e93cb90fe25cf *R/01_data_import.R
e8e515c95d8e47e61640a9dc51bed313 *R/02_data_preprocessing.R
77354420c01cd9240a86aa8203287a2d *R/03_similarity_searches.R
2d6891e7cc2e8ad79cf179d4563a1c0b *R/04_synteny_detection.R
e6084de621f04512584757b51d1f42ff *R/05_phylogenomic_profiling.R
f371c3f2e028be4218f27ff1fec8da00 *R/06_dataviz.R
6e66b39515553705a649f2cc0c9b53b4 *R/07_microsynteny-based_phylogeny.R
2ec32a433dc485a3e621a7b0a3089eff *R/RcppExports.R
541ff283c26c8ed6897a682fb24237be *R/catch-routine-registration.R
0ae964b7c6af38cfe7554d9ac35ac8fe *R/data.R
37dc259c92c2e99aa981511d2341a417 *R/syntenet-package.R
b9c79f691b1ff6d8621895b68d34aa1b *R/utils.R
ca46c34e99d60503195e8802f3e9d21a *R/utils_synteny.R
6acae69c76e3fbc583b973f81f2dc923 *README.md
e0fb39bd50abe44099fa4b3a6c8196af *build/vignette.rds
54ee66fc03b7ddd47c398258d454f723 *data/angiosperm_phylogeny.rda
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2f5a6ecc24b9d94a800fee9426d0a011 *data/blast_list.rda
133d79e0f5edbe0e0ffcf25fb20b3867 *data/clusters.rda
a2df9c38dedb63aab08cedad136e8e9d *data/datalist
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84d891c936ca488f02c4a7085c7e3544 *data/network.rda
b64b582f9720fe93832dbace63ec4d38 *data/proteomes.rda
5e994c2b28d51258f9a697bfc5d83c39 *data/scerevisiae_annot.rda
8b98109f06956f90ae522c0657e4ef40 *data/scerevisiae_diamond.rda
66dfdad58db43748a2627dd73875371c *inst/CITATION
dca803b2f96846a3bf2851ae593bba37 *inst/_pkgdown.yml
822016bc7c80a3056bd4deb7cdac412e *inst/doc/vignette_01_inference_and_analysis_of_synteny_networks.R
0ab5b034967f47b458c6244787826402 *inst/doc/vignette_01_inference_and_analysis_of_synteny_networks.Rmd
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b256e20a0994102bb990b2e2e4290ca4 *inst/extdata/Osp_Osp.tsv
8200b1fcd5808b4440a06feb1571f999 *inst/extdata/RefSeq_parsing_example/Aalosa.fa.gz
233cd8877aaac87cfba7b9b092283dbc *inst/extdata/RefSeq_parsing_example/Aalosa.gff3.gz
ea47e98d348e0c73d2ff8967cadfce92 *inst/extdata/Scerevisiae.collinearity
11292b9c17458c44567f2fd980bce2cf *inst/extdata/annotation/Olucimarinus.gff3.gz
16ad507b533946c5e58512b81cc9a36b *inst/extdata/annotation/OspRCC809.gff3.gz
ef17b09a2e237d8e606de9eb92b2085e *inst/extdata/sequences/Olucimarinus.fa.gz
c0b7dc960be17bc319e3418c6500c4e8 *inst/extdata/sequences/OspRCC809.fa.gz
12135fa4cdbea186b98dd88ca3a47bce *inst/script/data_acquisition.md
97bf7fd5fbd1d3f992f7af05b88b1b8c *man/angiosperm_phylogeny.Rd
96f763763796e199d476e238c0893a2e *man/annotation.Rd
4ed9ec02a69187d94a786c15a02b0516 *man/binarize_and_transpose.Rd
4c933a1dd376624f4cecffb3d2c88f45 *man/blast_list.Rd
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17d84fa9843800732bd1612ab5085fbc *man/collapse_bidirectional_hits.Rd
53a34772e41b5ae99036fd040ca27c0c *man/collapse_protein_ids.Rd
a91483e16cb3c5c367aba00a63a2c2dc *man/create_species_id_table.Rd
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3377dc20c8a3add09776fdc203a7b1c9 *man/export_sequences.Rd
74f2ef54f2d1de60a5e2c62c1bd9a293 *man/fasta2AAStringSetlist.Rd
020e42f5362cc063f1d0a534789255d5 *man/figures/logo.png
0215c6762c59caa553eed433197580f9 *man/find_GS_clusters.Rd
b49801a58678d4068c20839bc0a3ac7e *man/gff2GRangesList.Rd
7993d39cdaae8227877a23cc7eba9218 *man/infer_microsynteny_phylogeny.Rd
e1edfe6d4b4b59d0e189865ff5c92e16 *man/infer_syntenet.Rd
7c861c09f7ba63045a45c4c7b0334938 *man/interspecies_synteny.Rd
3e3245f68e93c16034c161e5080ae02d *man/intraspecies_synteny.Rd
ef7c69137c12910938f17a220a27c8b9 *man/iqtree_is_installed.Rd
2ca2ea0265ef856a3ffe5260bac46614 *man/iqtree_version.Rd
194e8ca2acaf64604cbadaeaa94d5547 *man/last_is_installed.Rd
5ed5818fe9e289ad4d226fc0715b7e8d *man/make_bidirectional.Rd
5dc7b8efb90a1c66014bad1cb239217f *man/network.Rd
34abbf1e3207f740d9f5b30b53d42b26 *man/parse_collinearity.Rd
b56df4aec1e3a39f88b90f1a02e77108 *man/phylogenomic_profile.Rd
be23abe0569e5008ee29a7844a44d4e2 *man/plot_network.Rd
35cf393779b8b7c7b1100849e1c3b42e *man/plot_profiles.Rd
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72dca9b72c68df7cf93b8e8e36f8c5c4 *man/proteomes.Rd
24e98a4a721da36ccfb611e9f65298ef *man/rcpp_mcscanx_file.Rd
a735a3a7afb9567a4386e700ef2f9ee0 *man/read_diamond.Rd
71643de321882bf33ef444c79fe9105d *man/run_diamond.Rd
dd08f4b82a741ea43df65ffaa4093012 *man/run_last.Rd
d8fe2cac07bc86f2edfecca9254d2bcc *man/scerevisiae_annot.Rd
5e428f4fe8278650a92ea0d8ed205105 *man/scerevisiae_diamond.Rd
2cbf09a9eb2b182bd15f6382d0de00a4 *man/syntenet-package.Rd
6dd36ec04333168fa865e5766133b246 *src/RcppExports.cpp
add80925548833280b2944fbfb35398d *src/mcscanxr.cpp
ce78db7d56cbeeca6717619a9e95e864 *src/mcscanxr.h
c2cb0c30e10da611f9fbe56aea52f7a9 *src/test-runner.cpp
1451bf7f9bf955f7cc1de8aca50aeb54 *tests/testthat.R
84bab6fda1802c93e15aded43e97c29d *tests/testthat/test-01_data_import.R
5c3833813f643594073b095e03977555 *tests/testthat/test-02_data_preprocessing.R
a0703c93a2cbe66ecddbd94c04a20dec *tests/testthat/test-03_synteny_detection.R
15867f5faa2386070031a2f5f1251a89 *tests/testthat/test-04_phylogenomic_profiling.R
01fd4f685727459c8147874ce8487a0c *tests/testthat/test-05_dataviz.R
cc7abd2f838e1cadad8c1b07f1938d0b *tests/testthat/test-06_microsynteny-based_phylogeny.R
5a2619d4422f94ab47264bbd847b0672 *tests/testthat/test-cpp.R
69c1f7fb0668d3219c4bc7fae4159a66 *tests/testthat/test-similarity_searches.R
51b3cd8390c32ce2dc61625c3851d381 *tests/testthat/test-utils.R
0ab5b034967f47b458c6244787826402 *vignettes/vignette_01_inference_and_analysis_of_synteny_networks.Rmd
bcd6fc61f30b9e4d63bd1af400fbc2c7 *vignettes/vignette_02_synteny_detection_with_syntenet.Rmd
5143175142f7ec5545b276a5d28d4602 *vignettes/vignette_bibliography.bib
