A web app and library for visualising and comparing phylogenetic trees.
The app can be accessed at beta.phylo.io.
For any bugs, features requests or help for integration please contact us through github.
Easy: Import all the pre generated js files from the dist/ folder. The font folder inside is mandatory.
<script src="path/to/dist/phylo.js"></script>
<!-- Import each other .js files from the dist/ folder.
Replace __filename__.js by each real filename -->
<script src="path/to/dist/__filename__.js"></script>Local build: You can build the package from source using the following command
npm run-script buildThen, you just to need import the freshly built phylo.js as shown previously.
Attention, it will also generate a folder named fonts that needs to be in the same folder as phylo.js
First, you need to create an instance of PhyloIO:
const phylo = PhyloIO.init() Then, you need to instantiate a container (or viewer) inside a div:
const c1 = phylo.create_container("div_id")If you want to compare several trees, you need to provide two containers:
const c1 = phylo.create_container("div_id_1")
const c2 = phylo.create_container("div_id_2")
// Required parameters for compare mode
phylo.settings.compareMode = true;
phylo.bound_container = [c1,c2];Optional: you can already add trees into containers
const newick1 = "((yli:1.0085614391793067,(((lel:0.2880678599618948,(cal:0.11643570498932501,ctr:0.12746420698315983):0.0877413194006926):0.12449843844102518,pst:0.20187483296288805):0.04951181210826987,(pgu:0.3208350693977453,dha:0.19121342958249643):0.0444880656387921):0.3761988962574594):0.22545281705785974,(((kla:0.32829009627835226,ago:0.35217085340006204):0.057415467336693615,(skl:0.15813405639248146,kwa:0.25658337062111586):0.04348414441988464):0.036897766465122404,(cgl:0.29957965624763355,(sca:0.24212307199678842,(sba:0.03984952076326609,(((sce:0.022286259220280224,spa:0.016875934069075366):0.01282179619059339,smi:0.03661027033511007):0.013312280806766753,sku:0.042685124078088485):0.014142671709463695):0.17548658899657893):0.03625000527459598):0.08921537612721808):0.22545281705785974):0;"
const newick2 = 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c1.add_tree(newick1, {'use_branch_lenght': true, 'name': 'tree #1'})
c2.add_tree(newick2)Here are settings you can specify when adding a tree:
'display_leaves' : true,
'mirror': false,
'name': null,
'data_type' : 'newick',
'use_branch_lenght' : true,
'show_tooltips' : false,
'subsample_label' : true,
'display_duplication' : false,
'display_internal_label' : false,
'display_internal_label_left_top' : false,
'display_internal_label_left_bottom' : false,
'align_tip' : false,
'display_leaves' : true,Finally, you can start phylo.io:
phylo.start()As shown in 'Examples/Phylo Stack', you can display phylostratigraphy viewer by doing:
var custom_settings = {
'name': 'phylostratigraphy',
'data_type' : 'json',
'use_branch_lenght' : false,
'show_histogram' : true,
'has_histogram_data' : true,
'stack' : {
'type': 'genes',// or 'events',
'showHistogramValues' : false,
'showHistogramSummaryValue' : true,
'legendTxtSize' : 12,
'margin' : 8,
'xInitialRightMargin' : 25,
'stackHeight' : 50,
'stackWidth' : 50,
'maxStackHeight': 'max', // ratio -> stack height fixed | max -> largest data = stack height
},
}
const tree_stack = {"children": [{"children": [{"children": [{"children": [{"id": "HALHT", "last_updated": "Aug 20, 2012", "name": "Haloarcula hispanica (strain ATCC 33960 / DSM 4426 / JCM 8911 / NBRC 102182 / NCIMB 2187 / VKM B-1755)", "nr_proteins": 3855, "release": "18-OCT-2011 (Rel. 110, Last updated, Version 2)", "source": "EBI", "taxid": 634497}, {"id": "HALMA", "last_updated": "Mar 25, 2014", "name": "Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)", "nr_proteins": 4231, "release": "02-FEB-2014 (Rel. 119, Last updated, Version 9)", "source": "EBI", "taxid": 272569}], "name": "Haloarcula", "taxid": 2237, "nr_hogs": 4107, "evolutionaryEvents": {"gained": 178, "retained": 3532, "duplicated": 397, "lost": 1508, "duplications": 166}}, {"id": "HALMD", "last_updated": "Nov 23, 2009", "name": "Halomicrobium mukohataei (strain ATCC 700874 / DSM 12286 / JCM 9738 / NCIMB 13541)", "nr_proteins": 3168, "release": "03-NOV-2009 (Rel. 113, Last updated, Version 1)", "source": "Genome Reviews", "taxid": 485914}, {"id": "HALUD", "last_updated": "Nov 23, 2009", "name": "Halorhabdus utahensis (strain DSM 12940 / JCM 11049 / AX-2)", "nr_proteins": 2998, "release": "03-NOV-2009 (Rel. 113, Last updated, Version 1)", "source": "Genome Reviews", "taxid": 519442}, {"children": [{"id": "NATM8", "last_updated": "Oct 27, 2014", "name": "Natronomonas moolapensis (strain DSM 18674 / JCM 14361 / 8.8.11)", "nr_proteins": 2852, "release": "27-FEB-2014 (Rel. 119, Last updated, Version 4)", "source": "EBI", "taxid": 268739}, {"id": "NATPD", "last_updated": "Mar 25, 2014", "name": "Natronomonas pharaonis (strain ATCC 35678 / DSM 2160 / CIP 103997 / NBRC 14720 / NCIMB 2260 / Gabara)", "nr_proteins": 2824, "release": "07-MAR-2014 (Rel. 120, Last updated, Version 14)", "source": "EBI", "taxid": 348780}], "name": "Natronomonas", "taxid": 63743, "nr_hogs": 3156, "evolutionaryEvents": {"gained": 93, "lost": 2294, "duplicated": 254, "retained": 2809, "duplications": 103}}], "name": "Haloarculaceae", "taxid": 1963268, "nr_hogs": 5206, "evolutionaryEvents": {"gained": 273, "retained": 4584, "duplicated": 349, "lost": 1040, "duplications": 163}}, {"children": [{"id": "HALJB", "last_updated": "Dec 23, 2010", "name": "Halalkalicoccus jeotgali (strain DSM 18796 / CECT 7217 / JCM 14584 / KCTC 4019 / B3)", "nr_proteins": 3779, "release": "30-NOV-2010 (Rel. 127, Last updated, Version 2)", "source": "Genome Reviews", "taxid": 795797}, {"children": [{"id": "HALS3", "last_updated": "May 8, 2008", "name": "Halobacterium salinarum (strain ATCC 29341 / DSM 671 / R1)", "nr_proteins": 2742, "release": "29-APR-2008 (Rel. 90, Last updated, Version 1)", "source": "Genome Reviews", "taxid": 478009}, {"id": "HALSA", "last_updated": "Mar 25, 2014", "name": "Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)", "nr_proteins": 2418, "release": "03-FEB-2014 (Rel. 119, Last updated, Version 7)", "source": "EBI", "taxid": 64091}], "name": "Halobacterium salinarum", "taxid": 2242, "nr_hogs": 2540, "evolutionaryEvents": {"gained": 201, "retained": 2202, "duplicated": 137, "lost": 1437, "duplications": 62}}], "name": "Halobacteriaceae", "taxid": 2236, "nr_hogs": 3701, "evolutionaryEvents": {"gained": 13, "retained": 3605, "duplicated": 83, "lost": 2142, "duplications": 40}}], "name": "Halobacteriales", "taxid": 2235, "nr_hogs": 5787, "evolutionaryEvents": {"gained": 118, "retained": 5120, "lost": 1677, "duplicated": 549, "duplications": 228}}, {"children": [{"children": [{"children": [{"id": "HALMT", "last_updated": "Nov 30, 2012", "name": "Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4)", "nr_proteins": 3861, "release": "02-AUG-2012 (Rel. 113, Last updated, Version 3)", "source": "EBI", "taxid": 523841}, {"id": "HALVD", "last_updated": "Jul 20, 2010", "name": "Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2)", "nr_proteins": 3986, "release": "13-JUL-2010 (Rel. 123, Last updated, Version 2)", "source": "Genome Reviews", "taxid": 309800}], "name": "Haloferax", "taxid": 2251, "nr_hogs": 4166, "evolutionaryEvents": {"gained": 107, "retained": 3786, "lost": 1192, "duplicated": 273, "duplications": 108}}, {"id": "HALBP", "last_updated": "Aug 20, 2012", "name": "Halogeometricum borinquense (strain ATCC 700274 / DSM 11551 / JCM 10706 / PR3)", "nr_proteins": 3894, "release": "24-NOV-2010 (Rel. 106, Last updated, Version 1)", "source": "EBI", "taxid": 469382}, {"children": [{"id": "HALWD", "last_updated": "Sep 26, 2006", "name": "Haloquadratum walsbyi (strain DSM 16790 / HBSQ001)", "nr_proteins": 2819, "release": "24-JUL-2006 (Rel. 88, Last updated, Version 2)", "source": "EBI", "taxid": 362976}, {"id": "HALWC", "last_updated": "Apr 2, 2012", "name": "Haloquadratum walsbyi (strain DSM 16854 / JCM 12705 / C23)", "nr_proteins": 2974, "release": "15-MAR-2012 (Rel. 112, Last updated, Version 4)", "source": "EBI", "taxid": 768065}], "name": "Haloquadratum walsbyi", "taxid": 293091, "nr_hogs": 2819, "evolutionaryEvents": {"gained": 209, "retained": 2443, "lost": 2564, "duplicated": 167, "duplications": 79}}], "name": "Haloferacaceae", "taxid": 1644056, "nr_hogs": 5086, "evolutionaryEvents": {"gained": 222, "duplicated": 385, "retained": 4479, "lost": 571, "duplications": 174}}, {"id": "HALLT", "last_updated": "Jun 22, 2009", "name": "Halorubrum lacusprofundi (strain ATCC 49239 / DSM 5036 / JCM 8891 / ACAM 34)", "nr_proteins": 3493, "release": "16-JUN-2009 (Rel. 107, Last updated, Version 3)", "source": "Genome Reviews", "taxid": 416348}], "name": "Haloferacales", "taxid": 1644055, "nr_hogs": 5224, "evolutionaryEvents": {"gained": 94, "retained": 4671, "lost": 2155, "duplicated": 459, "duplications": 199}}, {"children": [{"id": "HALXS", "last_updated": "Aug 20, 2012", "name": "Halopiger xanaduensis (strain DSM 18323 / JCM 14033 / SH-6)", "nr_proteins": 4221, "release": "23-NOV-2011 (Rel. 110, Last updated, Version 2)", "source": "EBI", "taxid": 797210}, {"id": "HALTV", "last_updated": "Jun 11, 2010", "name": "Haloterrigena turkmenica (strain ATCC 51198 / DSM 5511 / NCIMB 13204 / VKM B-1734)", "nr_proteins": 3739, "release": "25-MAY-2010 (Rel. 121, Last updated, Version 2)", "source": "Genome Reviews", "taxid": 543526}, {"id": "HALRX", "last_updated": "Dec 18, 2013", "name": "Halovivax ruber (strain DSM 18193 / JCM 13892 / XH-70)", "nr_proteins": 3099, "release": "18-JUL-2013 (Rel. 117, Last updated, Version 2)", "source": "EBI", "taxid": 797302}, {"children": [{"id": "NATA1", "last_updated": "Aug 10, 2017", "name": "Natrialba asiatica (strain ATCC 700177 / DSM 12278 / JCM 9576 / FERM P-10747 / NBRC 102637 / 172P1)", "nr_proteins": 4176, "release": "Ensembl Bacteria 36; ASM33755v1", "source": "EnsemblGenomes", "taxid": 29540}, {"id": "NATMM", "last_updated": "Jul 20, 2010", "name": "Natrialba magadii (strain ATCC 43099 / DSM 3394 / CIP 104546 / JCM 8861/ NBRC 102185 / NCIMB 2190 / MS3)", "nr_proteins": 3558, "release": "13-JUL-2010 (Rel. 123, Last updated, Version 2)", "source": "Genome Reviews", "taxid": 547559}], "name": "Natrialba", "taxid": 63742, "nr_hogs": 4283, "evolutionaryEvents": {"gained": 51, "lost": 2216, "retained": 3820, "duplicated": 412, "duplications": 148}}, {"children": [{"id": "NATP1", "last_updated": "Oct 27, 2014", "name": "Natrinema pellirubrum (strain DSM 15624 / CIP 106293 / JCM 10476 / NCIMB 786 / 157)", "nr_proteins": 4138, "release": "23-JUL-2013 (Rel. 117, Last updated, Version 2)", "source": "EBI", "taxid": 797303}, {"id": "NATSJ", "last_updated": "Oct 27, 2014", "name": "Natrinema sp. (strain J7-2)", "nr_proteins": 4296, "release": "15-MAY-2014 (Rel. 120, Last updated, Version 6)", "source": "EBI", "taxid": 406552}], "name": "Natrinema", "taxid": 88723, "nr_hogs": 4304, "evolutionaryEvents": {"gained": 52, "retained": 3748, "lost": 2241, "duplicated": 504, "duplications": 195}}, {"id": "NATGS", "last_updated": "Oct 27, 2014", "name": "Natronobacterium gregoryi (strain ATCC 43098 / DSM 3393 / CCM 3738 / CIP 104747 / JCM 8860 / NBRC 102187 / NCIMB 2189 / SP2)", "nr_proteins": 3624, "release": "18-JUL-2013 (Rel. 117, Last updated, Version 2)", "source": "EBI", "taxid": 797304}], "name": "Natrialbaceae", "taxid": 1644061, "nr_hogs": 6184, "evolutionaryEvents": {"gained": 842, "duplicated": 729, "retained": 4613, "lost": 2106, "duplications": 306}}], "name": "Halobacteria", "taxid": 183963, "nr_hogs": 7025, "evolutionaryEvents": {"gained": 2357, "lost": 6118, "retained": 2767, "duplicated": 1901, "duplications": 605}}
c1.add_tree(tree_stack,custom_settings)
phylo.start()