metaphlan 4
I would like to construct a phylogenetic tree corresponding to Metaphlan 4 taxonomy results. I have not been able to find a newick tree for Metaphlan 4.
Is the newick tree from Metaphlan 3 compatible with Metaphlan 4 for this?
Is there a Metaphlan command for creating a phylogenetic tree?
Hi @reaset41
You can find the tree here: MetaPhlAn/mpa_vJan21_CHOCOPhlAnSGB_202103.nwk at master · biobakery/MetaPhlAn · GitHub
If I reed the file in R with read_tree {from phyloseq} and inspect the object with mpa_tree$tip.label I obtain only numbers
[1] “87903” “77821” “2406” “2405” “77822” “77819” “27887” “77828” “27888” “2407” “2408” “63416” “36273” “35491” “21384” “79383” “21385”
[18] “27889” “79382” “2403” “2404” “21383” “35481” “27885” “79378” “21386” “79379” “49843” “21541” “21540” “27901” “2394” “27903” “27902”
[35] “2398” “27905” “21545” “35427” “27906” “2400” “27904” “21418” “27899” “77871” “2389” “77872” “27891” “49844” “27890” “84915” “27894”
[52] “27892” “27893” “21543” “27896” “27895” “84913” “84914” “27898” “2412” “2410” “2411” “21544” “21417” “35906” “40230” “35908” “35910”
[69] “40231” “35909” “40229” “35916” “40247” “35915” “35920” “35912” “40237” “35917” “35921” “35918” “40265” “35924” “35925” “40269” “35926”
[86] “35923” “40219” “48221” “2025” “2024” “2021” “70252” “2023” “2020” “48210” “48209” “58496” “2111” “40352” “40327” “40313” “40312”
[103] “48242” “40317” “48219” “48218” “2113” “40324” “58508” “40318” “2103” “21449” “35937” “2104” “40321” “40323” “2107” “40326” “35935”
[120] “2115” “40319” “40315” “40309” “40310” “2077” “2076” “20188” “2075” “2128” “27767” “2127” “63920” “2126” “21441” “2124” “21428”
[137] “2133” “2135” “40306” “40307” “2131” “2132” “40369” “40368” “2122” “2121” “2114” “48240” “35933” “70331” “21431” “40361” “2138”
[154] “63918” “2093” “40359” “40363” “2092” “2083” “2082” “40362” “21585” “21450” “21584” “40357” “40356” “2090” “2091” “2087” “40345”
[171] “2088” “35903” “63913” “2085” “2084” “40344” “21436” “27771” “40300” “2136” “27766” “2120” “21440” “20192” “48216” “48215” “40342”
[188] “21446” “40333” “40340” “2089” “40338” “21443” “2119” “21445” “27768” “48233” “35930” “2118” “2094” “48227” “2095” “2146” “27763”
[205] “2143” “2158” “2162” “2166” “2164” “2161” “2160” “48260” “35950” “2168” “40294” “2141” “40293” “40289” “48258” “40285” “27761”
[222] “2149” “40283” “35952” “40287” “2171” “2169” “35953” “2153” “2155” “2154” “20183” “20184” “2173” “40295” “48256” “2175” “2068”
[239] “2071” “2069” “2073” “2072” “48211” “2067” “1969” “1953” “1954” “1961” “1963” “1962” “1957” “1958” “1959” “1967” “1966”
[256] “1968” “1965” “1964” “1745” “40705” “1750” “1746” “35746” “40737” “35745” “27719” “35744” “1748” “27721” “1743” “35757” “40715”
[273] “35759” “35758” “35754” “69085” “35752” “35756” “40701” “40702” “40732” “35761” “35762” “35749” “35773” “35770” “40630” “27718” “40654”
[290] “1744” “40650” “40638” “69087” “40640” “35769” “35768” “40634” “35741” “40620” “35727” “35729” “35728” “35725” “40661” “35724” “1726”
[307] “40665” “1606” “40668” “1734” “35730” “40687” “40680” “40691” “40695” “35739” “35738” “40694” “1740” “1741” “40678” “35734” “35763”
[324] “40611” “35742” “35780” “35779” “40582” “40581” “35774” “40563” “35785” “35777” “35776” “1581” “29647” “1580” “35722” “40602” “35784”
[341] “35711” “35709” “35710” “40545” “35713” “35708” “35715” “35714” “35716” “40606” “40607” “35765” “40601” “35674” “40528” “40594” “40595”
[358] “40562” “35706” “40573” “35781” “35718” “35717” “35719” “1524” “1525” “1522” “1521” “1520” “21553” “1533” “3322” “35698” “40763”
[375] “1704” “1702” “20130” “1701” “1692” “35692” “35691” “1568” “1566” “1567” “1705” “20138” “35693” “35694” “1688” “1506” “1505”
[392] “1502” “1532” “35682” “1684” “1529” “35705” “20152” “1666” “1530” “21554” “35786” “27726” “1552” “1547” “1545” “1544” “1556”
[409] “1543” “1540” “1542” “1539” “1541” “1565” “1557” “1558” “1559” “27876” “1564” “1561” “1560” “1563” “27871” “27853” “1503”
[426] “1504” “27852” “20128” “1699” “1685” “35701” “35702” “1579” “35648” “1697” “27716” “1531” “1715” “35656” “40772” “27724” “1500”
[443] “20121” “1617” “20122” “1636” “1626” “1644” “1653” “20123” “1623” “1614” “1612” “20113” “1613” “1710” “1657” “1714” “35678”
[460] “1680” “1679” “1672” “1670” “1667” “1676” “1675” “27424” “1677” “1673” “20142” “1668” “20101” “20102” “1664” “1663” “1662”
[477] “1604” “40523” “1590” “1595” “1596” “1592” “1593” “20077” “20085” “27717” “1586” “1585” “1587” “1588” “48271” “1589” “21581”
[494] “1600” “1601” “40522” “1711” “1712” “70177” “1584” “20042” “40520” “1517” “1507” “1527” “1526” “3323” “1535” “1536” “1534”
[511] “1457” “1458” “1456” “1455” “1454” “1528” “40526” “35673” “35675” “35676” “35677” “1538” “35669” “35670” “35667” “35668” “40434”
[528] “35666” “1488” “48279” “35665” “27762” “20006” “35830” “35829” “35831” “40500” “35804” “35721” “40495” “20007” “1437” “48411” “35800”
[545] “70215” “40484” “35799” “70213” “40486” “40492” “70217” “40483” “35801” “35720” “40475” “70209” “40498” “40499” “35807” “40511” “40509”
[562] “40506” “35806” “40514” “1796” “1799” “1798” “1797” “40803” “1795” “65710” “40406” “35833” “21455” “35834” “35798” “1411” “1485”
[579] “48203” “1475” “1476” “1474” “1478” “1473” “27410” “1477” “1471” “1482” “1481” “65708” “20040” “48197” “48200” “48437” “21582”
[596] “40412” “48201” “48195” “1472” “48196” “1423” “1424” “1465” “1464” “1463” “1466” “1469” “1468” “1467” “27854” “35595” “35639”
[613] “35836” “1415” “40416” “40414” “20035” “40407” “1408” “1407” “20038” “20037” “1404” “35664” “35826” “70027” “35825” “35652” “35651”
[630] “1493” “40452” “48410” “70051” “70050” “35814” “35813” “35823” “35824” “35820” “35821” “40460” “35810” “35811” “35815” “48409” “40470”
[647] “40465” “40471” “35817” “35816” “35818” “35819” “1487” “20004” “1416” “1877” “27808” “3321” “77863” “1878” “69998” “1867” “1871”
[664] “27814” “48548” “1808” “1863” “1862” “1860” “1861” “1807” “1857” “1858” “1802” “1853” “1855” “77848” “77851” “77856” “77849”
[681] “27900” “1386” “1926” “1924” “27747” “27746” “48431” “1806” “1842” “1844” “1846” “1848” “1850” “40817” “1836” “1839” “21590”
[698] “21589” “1835” “1819” “1824” “1822” “1821” “65714” “65713” “1920” “77807” “1827” “1832” “1830” “1829” “1831” “1828” “48432”
[715] “1840” “1430” “1429” “1805” “1913” “1917” “1919” “1916” “1915” “1914” “1887” “1894” “1895” “1891” “1890” “1818” “1912”
[732] “1909” “1910” “1903” “63885” “1886” “1896” “1897” “1898” “1889” “1888” “1883” “1880” “48439” “1815” “1814” “1813” “1812”
[749] “27748” “40399” “2052” “35654” “40397” “35653” “35590” “70231” “35640” “40377” “40380” “35641” “40375” “40379” “35645” “48415” “48416”
[766] “48414” “58512” “35597” “48186” “35589” “35593” “35592” “35591” “52333” “35838” “70379” “1980” “1973” “1981” “1977” “2063” “2064”
[783] “2016” “2019” “2018” “3324” “2037” “2038” “2036” “2040” “2043” “2042” “2041” “1395” “2058” “2059” “2055” “21591” “2056”
[800] “2057” “2062” “1985” “1990” “27850” “1991” “27847” “2060” “2061” “1943” “1949” “1948” “1945” “21630” “1941” “1940” “1939”
[817] “1937” “1942” “1935” “21587” “1951” “1432” “1928” “1930” “1931” “20171” “1933” “63877” “77766” “1934” “27780” “27749” “27839”
[834] “1927” “2051” “2050” “77855” “27832” “2047” “2048” “2053” “27842” “25797” “35466” “35465” “2003” “21424” “1999” “35464” “2010”
[851] “2009” “27829” “2008” “35463” “1995” “21423” “35459” “77850” “27827” “84923” “35432” “1774” “27837” “27835” “77857” “48073” “77858”
[868] “1772” “27838” “21566” “27834” “84922” “1769” “1770” “77859” “3317” “28850” “35633” “39866” “35624” “35625” “35626” “35621” “39869”
[885] “35631” “35616” “35630” “35634” “35628” “35617” “35618” “39876” “35615” “35632” “39855” “35614” “39848” “35612” “39844” “39843” “35605”
[902] “35606” “48177” “35611” “35609” “35599” “39894” “35598” “39901” “35635” “48179” “48178” “1371” “19980” “19979” “1370” “19974” “19973”
[919] “19975” “19976” “48175” “35608” “19971” “36709” “70246” “1344” “1343” “1341” “48188” “48182” “48184” “48183” “48160” “63962” “77869”
[936] “1346” “27841” “77835” “63564” “35478” “77763” “77761” “1348” “1777” “1776” “1778” “27742” “1785” “1786” “1784” “1783” “1782”
[953] “1781” “40789” “40793” “1789” “1790” “40792” “1792” “1791” “40791” “77713” “39990” “35532” “35535” “35533” “35534” “35521” “35522”
[970] “35523” “35530” “35525” “35528” “35527” “35531” “35538” “35536” “40026” “40021” “35539” “35512” “39966” “40016” “40065” “35510” “39938”
[987] “40019” “35542” “35544” “39946” “35516” “35513” “39956” “35515” “39960” “70451” “39954” “35519” “20235” “2229”
[ reached getOption(“max.print”) – omitted 25931 entries ]
Is there any method to change the number to taxa names?
Hi @imontero the numbers are basically the SGB ids, you can get the species identification from the *species.txt files available here: Index of /biobakery4/metaphlan_databases
Thank you for the link.
Am I right that this tree is already rooted?