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bouckaert_et_al2012
bouckaert_et_al2018
bowern_and_atkinson2012
chacon_and_list2015
chang_et_al2015
dunn_et_al2011_utoaztecan
glottolog_abkh1242
glottolog_afro1255
glottolog_ainu1252
glottolog_algi1248
glottolog_anim1240
glottolog_arau1255
glottolog_araw1281
glottolog_atha1245
glottolog_atla1278
glottolog_aust1305
glottolog_aust1307
glottolog_ayma1253
glottolog_barb1265
glottolog_boro1281
glottolog_cadd1255
glottolog_cari1283
glottolog_cent2225
glottolog_chib1249
glottolog_chim1311
glottolog_chin1490
glottolog_choc1280
glottolog_chon1288
glottolog_chuk1271
glottolog_chum1262
glottolog_coch1271
glottolog_coos1248
glottolog_dizo1235
glottolog_dogo1299
glottolog_drav1251
glottolog_east2386
glottolog_east2499
glottolog_east2503
glottolog_eski1264
glottolog_fura1235
glottolog_global
glottolog_goil1242
glottolog_gong1255
glottolog_grea1241
glottolog_guah1252
glottolog_guai1249
glottolog_gunw1250
glottolog_haid1248
glottolog_heib1242
glottolog_hmon1336
glottolog_huav1256
glottolog_huit1251
glottolog_ijoi1239
glottolog_indo1319
glottolog_iroq1247
glottolog_japo1237
glottolog_jara1244
glottolog_jarr1235
glottolog_jica1245
glottolog_jiva1245
glottolog_jodi1234
glottolog_kadu1256
glottolog_kaku1242
glottolog_kart1248
glottolog_kawe1237
glottolog_kere1287
glottolog_khoe1240
glottolog_kiow1265
glottolog_kiwa1251
glottolog_koia1260
glottolog_kolo1268
glottolog_koma1264
glottolog_kore1284
glottolog_kwer1242
glottolog_kxaa1236
glottolog_lenc1239
glottolog_leng1261
glottolog_lowe1437
glottolog_maid1262
glottolog_mail1249
glottolog_mand1469
glottolog_mani1293
glottolog_maoo1243
glottolog_mata1289
glottolog_maya1287
glottolog_misu1242
glottolog_miwo1274
glottolog_mixe1284
glottolog_mong1329
glottolog_more1255
glottolog_musk1252
glottolog_nakh1245
glottolog_namb1299
glottolog_narr1279
glottolog_nduu1242
glottolog_nilo1247
glottolog_nort1547
glottolog_nort2923
glottolog_nubi1251
glottolog_nucl1580
glottolog_nucl1708
glottolog_nucl1709
glottolog_nucl1710
glottolog_nyim1244
glottolog_otom1299
glottolog_pala1350
glottolog_pama1250
glottolog_pano1259
glottolog_peba1241
glottolog_pomo1273
glottolog_quec1387
glottolog_saha1239
glottolog_saha1256
glottolog_sali1255
glottolog_sepi1257
glottolog_shas1238
glottolog_sino1245
glottolog_siou1252
glottolog_song1307
glottolog_sout1293
glottolog_sout2772
glottolog_sout2845
glottolog_sout2948
glottolog_surm1244
glottolog_taik1256
glottolog_tang1340
glottolog_tara1323
glottolog_tequ1244
glottolog_ticu1244
glottolog_timo1261
glottolog_toto1251
glottolog_tsim1258
glottolog_tuca1253
glottolog_tung1282
glottolog_tupi1275
glottolog_turk1311
glottolog_tuuu1241
glottolog_ural1272
glottolog_uruc1242
glottolog_utoa1244
glottolog_waka1280
glottolog_west1503
glottolog_wint1258
glottolog_worr1236
glottolog_yano1268
glottolog_yeni1252
glottolog_yoku1255
glottolog_yuka1259
glottolog_yuki1242
glottolog_zamu1243
gray_et_al2009
grollemund_et_al2015
honkola_et_al2013
kitchen_et_al2009
kolipakam_et_al2018
lee2015
lee_and_hasegawa2011
lee_and_hasegawa2013
michael_et_al2015
sicoli_and_holton2014
README.md
index.csv

README.md

Phylogenies

Each directory within the phylogenies subdirectory MUST contain the following:

  1. taxa.csv -- a csv file linking the taxon labels in summary.trees to their correct glottocodes and xd_ids and society ids:

    taxon glottocode xd_ids soc_ids

  2. summary.trees -- a single summary tree in nexus tree format.

And may contain other files including:

  1. original/ -- a directory storing the original tree files. Note: For programmatically created phylogenies like the ones from Glottolog, this directory is not present.

  2. posterior.trees -- a posterior probability distribution of the trees (if available) in nexus tree format.

  3. Makefile -- a Makefile to generate summary.trees and posterior.trees from the original data.

Prerequisites:

If you want to run the Makefiles yourself then you will need to install the python-nexus library for the nexus_treemanip.py program.

Notes on adding a new tree:

  • the directory name should reflect the source of the tree (e.g. gray_et_al2009) rather than the language family (e.g. austronesian.trees) as we might have multiple trees for the same language family, or trees that span families.
  • the directory should be lower case.
  • each directory must be added to index.csv