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phyloio

2.0.1 • Public • Published

Phylo.io

A web app and library for visualising and comparing phylogenetic trees.

Demo

The app can be accessed at beta.phylo.io.

Quick Start

Easy: import directly the phylo.js from CDN. It contains all phylo.io requires (.js, .css and font/icons)

<script src="https://cdn.jsdelivr.net/gh/DessimozLab/phylo-io@refactor/dist/phylo.js"></script>

Local build: You can build the package from source using the following command

npm run-script build

Then, you just to need import the freshly built phylo.js

<script src="path/to/dist/phylo.js"></script>

Attention, it will also generate a folder named fonts that needs to be in the same folder as phylo.js

Initialisation

First, you need to create an instance of PhyloIO:

    const  phylo = PhyloIO.init() 
    // Note that the instance must be called phylo

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];

Optionnal: 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 = "(((SOLTU34696:0.02229166687593289037,SOLLC24463:0.00709709081903918577):0.18421898265728259281,((((MEDTR17610:0.15714167879247994963,(SOYBN06937:0.02529940651188004874,SOYBN15364:0.00931421471673856902):0.03339587536636171722):0.04648572868545788189,(SOYBN40305:0.05161993270599975203,SOYBN06011:0.01868797976671805749):0.13262390593762377056):0.09574925506273131159,((POPTR14057:0.08501820169894380719,POPTR15493:0.03388172716526779982):0.04903132056086856316,(VITVI16878:0.15032892038600365048,(MANES09114:0.00455508973340297985,MANES09113:0.00000100000050002909):0.10960937493738516502):0.06005265654177237983):0.03327927635394690997):0.04169405035061653220,((((SELML14800:0.01085671843303792107,SELML05537:0.02039560840819776635):0.73478761253095836725,(((((((MUSAM01035:0.00000100000050002909,MUSAC06029:0.00000100000050002909):0.30554247145426172150,((((ARALY04176:0.03071803778508035501,ARATH04062:0.02390145058045729451):0.26881464177877639754,(ARATH20168:0.04620983006923840702,ARALY11148:0.00932022073022199457):0.20782072992434411085):0.09488068423975774823,(((SOYBN02845:0.00976170253766352886,SOYBN51173:0.02918590246006154409):0.08540209758062287937,((MEDTR41063:0.00000100000050002909,MEDTR41066:0.02017257537407208742):0.16176325397181906540,(SOYBN11067:0.03963088470198131846,SOYBN08966:0.01232745661039070031):0.08548569071631144378):0.04853822353702215431):0.14497593655405260904,(MANES12931:0.07738860904262530316,(MANES07497:0.09434645317867160208,POPTR11029:0.12695444105377301502):0.02979790056758981412):0.05775061588261572176):0.01638682789008762478):0.05403462689546538467,(((MUSAM29615:0.00000100000050002909,MUSAC32718:0.00000100000050002909):0.08299761701045121898,((MUSAM27485:0.00000100000050002909,MUSAC30588:0.00000100000050002909):0.06661990811446089067,(MUSAC19509:0.00000100000050002909,MUSAM13578:0.00000100000050002909):0.06965462171572417427):0.02546304953829388665):0.19603767643398820053,(SOLLC06707:0.01792241662639993890,SOLTU18103:0.01706502381760034368):0.18420517353108956105):0.02629729192908691893):0.18414179845688000148):0.53817024374636479589,((SELML06655:0.00000100000050002909,SELML08476:0.03320959111509765721):0.85020985387688086110,(SELML03696:0.00000100000050002909,SELML10004:0.00646896469865896381):0.70379805522375493698):0.08752580347866126265):0.06518214565099944569,(((SELML10585:0.09739496921243473437,((SELML09645:0.01874532851656703428,SELML09389:0.00461002747936521164):0.00923396102862936510,(((SELML20828:0.00466275631610225862,(((SELML20789:0.01052082189588285019,SELML01265:0.01037032025689046087):0.12574093071149400336,SELML20813:0.00000100000050002909):0.00927460510378439601,SELML09379:0.00932813396907514365):0.01397774234266347532):0.01871018274364625450,SELML09395:0.00000100000050002909):0.00000100000050002909,SELML20823:0.00463913170794102298):0.00475219553005659830):0.03038880589415450875):0.25057129550716489286,(SELML06902:0.00000100000050002909,SELML13410:0.01944383189133876144):0.69918435501807829624):0.21184059841609043096,(((SOLTU11560:0.00866375047195633470,SOLLC08801:0.03929176849985123454):0.10262341703543685634,(SOLTU05304:0.01187114169278406621,SOLLC33391:0.01633284173625539071):0.15173972504306554310):0.21239804572202647392,(((SOLLC08269:0.02116737660229363674,SOLTU10962:0.01372146392435308164):0.25856914038108191889,((((MEDTR21917:0.01799185381782565998,MEDTR21918:0.00922025508246283182):0.05573688941724050383,((SOYBN35782:0.03087107867875190509,SOYBN00680:0.01163081217349988539):0.08312081118311021033,MEDTR21916:0.15768887143629881087):0.03305450703309942284):0.01735157638851950873,((SOYBN01697:0.01802156549906810262,SOYBN46853:0.01038317775355940449):0.09530254205432765746,(SOYBN00679:0.02003726912435226451,SOYBN35783:0.03023646561760832269):0.03688686876344755838):0.02302672045433903220):0.08493744642431001746,((VITVI19452:0.12740781730937075777,((POPTR37828:0.04689316251484140774,POPTR22952:0.05970448316470000627):0.04193762972183705945,MANES11398:0.08400005523386327999):0.02628003046485331493):0.03551912761098192928,((((ARATH04782:0.00000100000050002909,ARALY08526:0.01228654282875111386):0.29212655156837918913,(ARATH15344:0.00223041658309429966,ARALY09276:0.01996073486554238163):0.13397468053224975693):0.07185417278801679852,POPTR16926:0.13312849254037534275):0.01098363254080201613,(MANES03104:0.09480815288204409719,MANES16408:0.02654262709927663472):0.03040210277567834823):0.03004035743504208933):0.01404570578236909867):0.03121249594034346958):0.05887160826170913935,(((SORBI10122:0.03323503849451007325,(MAIZE08377:0.02021590177517258030,SETIT28177:0.08805632675554768418):0.02504709626837576045):0.07287654177256396026,((BRADI21338:0.02686457952333810503,(WHEAT87462:0.01035700555682448655,(AEGTA26567:0.02910656260243310589,WHEAT48582:0.00000100000050002909):0.00625588989844735790):0.02544515824802914133):0.05168964740217039944,(ORYBR07284:0.04813817240195044506,(ORYSJ56422:0.00433527809312172531,(ORYGL06636:0.00000100000050002909,ORYSI08916:0.0043120440763912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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,
'align_tip' : false,

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()

/phyloio/

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