worldtree_replication.zip
worldtree_replication
README.md
6.8 kB
code
Manifest.toml
96.6 kB
Project.toml
1.6 kB
alignment_functions_phmm.jl
7.9 kB
analyze_misleading_chars.jl
15.9 kB
build_charmatrix_colmap.jl
3.4 kB
compare_glottolog.R
5.1 kB
construct_glottolog_tree.jl
2.0 kB
create_concept_study_matrices.jl
3.1 kB
create_msa_charmatrix.jl
4.4 kB
create_msas.jl
3.6 kB
create_njtrees.r
860 Bytes
determine_number_of_concepts.jl
5.3 kB
evaluate_rates.jl
2.0 kB
filter_charmatrix.jl
4.3 kB
filter_notonal_charmatrix.jl
3.0 kB
forward.jl
2.5 kB
forwardGradient.jl
5.4 kB
get_dellert_ranking.jl
2.0 kB
get_glottolog.jl
1.3 kB
get_ldn_distances.jl
3.0 kB
get_lexibank.jl
2.7 kB
levenshtein.jl
2.2 kB
mad.py
24.4 kB
make_worldtree_ultrametric.r
678 Bytes
optimize_phmm.jl
10.8 kB
phmm.jl
3.6 kB
phmm_dist.jl
7.0 kB
phmm_parameters.json
22.6 kB
plot_pythia_difficulty.R
2.2 kB
plot_pythia_difficulty.py
2.8 kB
plot_training.r
1.6 kB
plot_worldtree.R
7.8 kB
prepare_data.jl
4.4 kB
prune_wordlist.jl
833 Bytes
sound_probabilities.csv
1.1 kB
trace_asr_sites.R
7.0 kB
trace_misplacements.R
3.9 kB
viterbi.jl
2.4 kB
data
alignments
alignment_AND.csv
102.6 kB
alignment_ARM.csv
177.3 kB
alignment_ARROW.csv
121.1 kB
alignment_ASH.csv
1.0 MB
alignment_BARKING.csv
11.7 kB
alignment_BE ABLE.csv
11.7 kB
alignment_BE ALIVE.csv
277.9 kB
alignment_BECOME.csv
19.0 kB
alignment_BELLY.csv
813.8 kB
alignment_BITTER.csv
94.9 kB
alignment_BLACK.csv
811.2 kB
alignment_BLOOD.csv
1.3 MB
alignment_BOIL (OF LIQUID).csv
33.3 kB
alignment_BOIL (SOMETHING).csv
7.4 kB
alignment_BONE.csv
1.3 MB
alignment_BOW.csv
120.1 kB
alignment_BRANCH.csv
159.2 kB
alignment_BRIDGE.csv
42.0 kB
alignment_BRING.csv
22.0 kB
alignment_BURNING.csv
36.4 kB
alignment_BUTTER.csv
17.3 kB
alignment_BUY.csv
162.9 kB
alignment_CARRY.csv
120.7 kB
alignment_CATCH.csv
25.9 kB
alignment_CHEST.csv
137.0 kB
alignment_CLAW.csv
215.5 kB
alignment_COLD.csv
847.0 kB
alignment_COME.csv
1.8 MB
alignment_COVER.csv
39.5 kB
alignment_COW.csv
109.0 kB
alignment_CRY.csv
346.0 kB
alignment_CUT.csv
129.5 kB
alignment_DAUGHTER.csv
134.8 kB
alignment_DAY (NOT NIGHT).csv
364.6 kB
alignment_DEATH.csv
19.1 kB
alignment_DENSE.csv
10.8 kB
alignment_DIE.csv
1.8 MB
alignment_DIG.csv
286.9 kB
alignment_DIVIDE.csv
55.9 kB
alignment_DO.csv
62.2 kB
alignment_DOG.csv
1.5 MB
alignment_DOOR.csv
115.5 kB
alignment_DRAW MILK.csv
35.3 kB
alignment_DREAM.csv
32.5 kB
alignment_DRINK.csv
1.7 MB
alignment_DRIVE (CATTLE).csv
6.8 kB
alignment_DRIVE.csv
9.2 kB
alignment_DRY UP.csv
89.9 kB
alignment_DRY.csv
603.3 kB
alignment_EAR.csv
1.7 MB
alignment_EARTH (SOIL).csv
569.6 kB
alignment_EAT.csv
1.3 MB
alignment_EGG.csv
963.6 kB
alignment_END (OF SPACE).csv
9.2 kB
alignment_EYE.csv
1.6 MB
alignment_FALL.csv
451.2 kB
alignment_FATHER.csv
382.5 kB
alignment_FEATHER.csv
761.0 kB
alignment_FINGER.csv
181.7 kB
alignment_FINGERNAIL OR TOENAIL.csv
36.6 kB
alignment_FIRE.csv
1.4 MB
alignment_FISH.csv
1.3 MB
alignment_FIVE.csv
723.3 kB
alignment_FLOW.csv
124.0 kB
alignment_FLY (MOVE THROUGH AIR).csv
738.7 kB
alignment_FOAM.csv
38.7 kB
alignment_FOOT.csv
541.9 kB
alignment_FOOTPRINT.csv
11.9 kB
alignment_FOUR.csv
623.0 kB
alignment_FRINGE.csv
5.5 kB
alignment_FULL.csv
936.4 kB
alignment_GET.csv
35.3 kB
alignment_GIVE.csv
886.1 kB
alignment_GO.csv
197.0 kB
alignment_GOOD.csv
747.0 kB
alignment_GRAIN.csv
25.7 kB
alignment_GRASS.csv
275.8 kB
alignment_GROW.csv
132.4 kB
alignment_HAIR.csv
696.9 kB
alignment_HALF.csv
49.6 kB
alignment_HAND.csv
1.5 MB
alignment_HAY.csv
20.2 kB
alignment_HE.csv
34.1 kB
alignment_HEAD.csv
969.9 kB
alignment_HEAR.csv
1.6 MB
alignment_HEART.csv
653.0 kB
alignment_HERE.csv
124.3 kB
alignment_HOLD.csv
227.4 kB
alignment_HOME.csv
14.3 kB
alignment_HONEY.csv
92.5 kB
alignment_HORN (ANATOMY).csv
624.8 kB
alignment_HORSE.csv
99.7 kB
alignment_HOUSE.csv
328.5 kB
alignment_HUNDRED.csv
235.1 kB
alignment_I.csv
891.8 kB
alignment_ICE.csv
44.5 kB
alignment_IRON.csv
114.8 kB
alignment_KILL.csv
1.2 MB
alignment_KNEE.csv
1.7 MB
alignment_KNIFE.csv
201.3 kB
alignment_KNOW (SOMETHING).csv
362.6 kB
alignment_LAKE.csv
184.2 kB
alignment_LANGUAGE.csv
27.3 kB
alignment_LAUGH.csv
348.7 kB
alignment_LAY (VERB).csv
8.9 kB
alignment_LEAF.csv
1.5 MB
alignment_LEATHER.csv
13.5 kB
alignment_LEG.csv
222.1 kB
alignment_LICK.csv
51.7 kB
alignment_LIFE.csv
26.5 kB
alignment_LONG.csv
726.6 kB
alignment_LOUSE.csv
1.0 MB
alignment_MAKE.csv
16.0 kB
alignment_MEASURE.csv
12.5 kB
alignment_MEAT.csv
205.7 kB
alignment_MELT.csv
14.6 kB
alignment_MIDDLE.csv
40.4 kB
alignment_MILK.csv
179.2 kB
alignment_MONTH.csv
30.1 kB
alignment_MOON.csv
967.5 kB
alignment_MOTHER.csv
418.0 kB
alignment_MOUNTAIN.csv
1.1 MB
alignment_MOUTH.csv
751.2 kB
alignment_NAME.csv
1.4 MB
alignment_NEEDLE (FOR SEWING).csv
88.8 kB
alignment_NEST.csv
28.8 kB
alignment_NET.csv
8.7 kB
alignment_NEW.csv
1.3 MB
alignment_NIGHT.csv
1.8 MB
alignment_NOSE.csv
1.7 MB
alignment_NOT.csv
237.6 kB
alignment_OAR.csv
17.6 kB
alignment_OIL (ORGANIC SUBSTANCE).csv
22.5 kB
alignment_ONE.csv
1.6 MB
alignment_OPEN.csv
162.9 kB
alignment_OR.csv
7.3 kB
alignment_PAIN.csv
14.9 kB
alignment_PART.csv
17.7 kB
alignment_PATH OR ROAD.csv
195.9 kB
alignment_PAY.csv
40.8 kB
alignment_PLACE (POSITION).csv
33.5 kB
alignment_PRICE.csv
18.9 kB
alignment_PULL.csv
133.5 kB
alignment_RAIN (PRECIPITATION).csv
311.7 kB
alignment_RAW.csv
44.7 kB
alignment_READ.csv
35.8 kB
alignment_RIVER.csv
176.4 kB
alignment_ROOT.csv
941.3 kB
alignment_SALT.csv
334.9 kB
alignment_SAND.csv
831.4 kB
alignment_SAY.csv
635.0 kB
alignment_SEA.csv
220.8 kB
alignment_SEE.csv
1.5 MB
alignment_SELL.csv
86.9 kB
alignment_SEVEN.csv
475.1 kB
alignment_SEW.csv
206.9 kB
alignment_SIDE.csv
15.8 kB
alignment_SIT DOWN.csv
60.7 kB
alignment_SIT.csv
785.1 kB
alignment_SIX.csv
506.7 kB
alignment_SKIN.csv
1.7 MB
alignment_SKY.csv
449.6 kB
alignment_SLEEP (STATE).csv
39.3 kB
alignment_SLEEP.csv
1.1 MB
alignment_SMOKE (EXHAUST).csv
851.7 kB
alignment_SNOW.csv
63.8 kB
alignment_SON.csv
152.6 kB
alignment_SOUND OR NOISE.csv
12.4 kB
alignment_SPOIL (BECOME SPOILED).csv
7.3 kB
alignment_STAND.csv
799.7 kB
alignment_STONE.csv
1.3 MB
alignment_STRIKE (SOMETHING).csv
5.1 kB
alignment_SUMMER.csv
14.4 kB
alignment_SUN.csv
1.5 MB
alignment_TAKE.csv
106.0 kB
alignment_TEN.csv
545.1 kB
alignment_THAT.csv
515.2 kB
alignment_THAW (DEW).csv
5.7 kB
alignment_THERE.csv
136.9 kB
alignment_THEY.csv
432.7 kB
alignment_THING.csv
42.8 kB
alignment_THIS.csv
351.0 kB
alignment_THOU.csv
919.8 kB
alignment_THREAD.csv
39.3 kB
alignment_THREE.csv
671.9 kB
alignment_TIE.csv
193.3 kB
alignment_TIME.csv
44.2 kB
alignment_TONE (MUSIC).csv
4.9 kB
alignment_TONGUE.csv
1.6 MB
alignment_TOOTH.csv
1.6 MB
alignment_TREE.csv
1.4 MB
alignment_TWO.csv
1.4 MB
alignment_VOICE.csv
28.0 kB
alignment_WAIT (FOR).csv
65.4 kB
alignment_WASH.csv
191.7 kB
alignment_WATER.csv
1.2 MB
alignment_WE.csv
930.0 kB
alignment_WHAT.csv
701.5 kB
alignment_WHERE.csv
376.5 kB
alignment_WHITE.csv
909.7 kB
alignment_WHO.csv
659.5 kB
alignment_WIND.csv
463.2 kB
alignment_WING.csv
391.6 kB
alignment_WINTER.csv
16.1 kB
alignment_WOOD.csv
71.3 kB
alignment_WOOL.csv
27.1 kB
alignment_WORD.csv
44.4 kB
alignment_WRITE.csv
22.1 kB
alignment_YEAR.csv
246.0 kB
alignment_YOU.csv
357.1 kB
dellert_ranking.csv
16.0 kB
glottolog.tre
34.7 kB
glottolog_divergence.csv
3.9 kB
ldn_bionj.tre
129.1 kB
ldn_bionj.tre.rooted
123.0 kB
ldn_distances.csv
367.8 MB
lexibank_pruned_wordlist.csv
98.6 MB
misplaced_languages.csv
24.7 kB
phmm_bionj.tre
129.4 kB
phmm_distances.csv
365.3 MB
phylip
charmatrix_column_map.csv
2.2 MB
concepts_103.raxml.bestTree.rooted
112.9 kB
concepts_103_constrained.raxml.bestTree
98.5 kB
concepts_103_constrained.raxml.bestTree.rooted
113.2 kB
concepts_103_notonal.raxml.bestTree
98.5 kB
concepts_103_notonal.raxml.bestTree.rooted
112.8 kB
msa.phy
261.3 MB
msa_notonal.phy
300.0 MB
logs
cleo
analyze_misleading.log
393.7 kB
charmatrix_interactive.log
85 Bytes
colmap.log
888 Bytes
concept_study_matrices_20260326_072501.log
337 Bytes
concept_study_matrices_20260326_072549.log
49.4 kB
create_msa_charmatrix_20260326_070855.log
85 Bytes
create_msa_charmatrix_20260326_170415.log
85 Bytes
create_msas_20260322_164456.log
10.9 MB
filter_charmatrix_20260329_162953.log
2.1 kB
filter_charmatrix_20260329_163240.log
734 Bytes
filter_notonal.log
520 Bytes
pythia_20260326_080629.log
416 Bytes
pythia_20260326_080652.log
416 Bytes
pythia_launcher.log
205.5 kB
raxml_asr.log
3.4 kB
raxml_concepts103.log
6.3 kB
raxml_notonal.log
3.8 kB
ultrametric_20260330_093932.log
235 Bytes
swadesh
create_msas_backwards_20260324_112509.log
103.4 kB
create_msas_backwards_20260324_143754.log
159.8 kB
create_msas_backwards_20260324_145526.log
2.2 kB
create_msas_backwards_20260324_145602.log
2.2 kB
create_msas_backwards_20260324_150527.log
6.7 kB
create_msas_backwards_20260324_150825.log
7.5 MB
filter_msas_aliscore_20260329_160050.log
1.3 kB
filter_msas_aliscore_20260329_160156.log
1.3 kB
filter_msas_aliscore_20260329_160336.log
1.2 kB
filter_msas_aliscore_20260329_160528.log
1.9 kB
filter_msas_aliscore_20260329_160736.log
9.5 kB
filter_msas_aliscore_20260329_161039.log
9.7 kB
filter_msas_aliscore_20260329_162128.log
19.6 kB
raxml_constrained.log
6.0 kB
raxml_filtered.log
6.4 kB
paper
img
pythia_difficulty_plot.pdf
15.0 kB
worldtree_plot.pdf
367.4 kB
references.bib
8.0 kB
worldtree_2026_jaeger.aux
8.7 kB
worldtree_2026_jaeger.bbl
4.6 kB
worldtree_2026_jaeger.blg
926 Bytes
worldtree_2026_jaeger.log
26.1 kB
worldtree_2026_jaeger.out
2.0 kB
worldtree_2026_jaeger.pdf
533.2 kB
worldtree_2026_jaeger.synctex.gz
77.9 kB
worldtree_2026_jaeger.tex
26.6 kB
worldtree.ultrametric.nwk
127.5 kB
worldtree_constrained.ultrametric.nwk
133.4 kB
worldtree_msa.yml
405 Bytes
worldtree_notonal.ultrametric.nwk
127.0 kB