Suhanaser patch 3

datasets/Thiergart_2014b/README.yaml

@@ -0,0 +1,30 @@
+study:
+    reference: "Thiergart T, Landan G, Martin WF. 2014. Concatenated alignments and the case of the disappearing tree. BMC Evol. Biol. 14:266."
+    year: 2014
+    DOI: dx.doi.org/10.1186/s12862-014-0266-0
+
+dataset:
+    DOI: dx.doi.org/10.5061/dryad.06640
+    license: CC0
+    used for tree inference: yes
+    alignment:
+        ntax: 100
+        nchar: 28217
+        datatype: protein
+        partitions: 48
+    genomes:
+        mitochondrial: no
+        nuclear: no
+        chloroplast: no
+        dsDNA: no
+        ssDNA: no
+        dsRNA: no
+        ssRNA: no
+        bacterial: yes
+    timetree root age: 2910 mya
+    study root age: NA
+    study clade:
+        latin: "proteobacteria"
+        english: "proteobacteria"
+        taxon ID: 1224
+    notes: "This is the proteobacteria dataset with 48 genes, figure 1.B in the original paper"

datasets/Thiergart_2014b/alignment.nex-seq-summary.txt

@@ -0,0 +1,101 @@
+Alignment_name	Taxon_name	Sequence_length	Undetermined_characters	Missing_percent	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y	B	J	Z	X	.	*	-	?
+alignment.nex	uid41317	28217	10718	37.984	1741	140	1035	1186	630	1433	384	1060	865	1559	483	510	759	706	1258	884	924	1371	175	396	0	0	0	0	0	0	10718	0
+alignment.nex	uid41425	28217	10476	37.127	1708	169	1086	1368	587	1501	382	886	931	1572	436	473	791	554	1443	900	867	1415	197	475	0	0	0	0	0	0	10476	0
+alignment.nex	uid41861	28217	11204	39.707	1338	181	868	1405	714	1219	327	1247	1478	1464	444	730	592	505	819	951	786	1278	141	526	0	0	0	0	0	0	11204	0
+alignment.nex	uid42117	28217	10365	36.733	2037	109	1172	1212	618	1581	328	896	933	1512	419	493	870	566	1291	781	999	1417	217	401	0	0	0	0	0	0	10365	0
+alignment.nex	uid42613	28217	10855	38.47	1556	230	1056	1284	658	1444	345	984	1106	1517	504	533	764	530	1159	817	872	1368	184	451	0	0	0	0	0	0	10855	0
+alignment.nex	uid46083	28217	10656	37.764	1794	158	1064	1337	576	1486	368	979	846	1643	437	454	794	638	1404	777	868	1327	183	428	0	0	0	0	0	0	10656	0
+alignment.nex	uid46085	28217	10793	38.25	1862	130	1060	1237	581	1531	353	943	962	1552	449	483	819	514	1313	745	921	1386	190	393	0	0	0	0	0	0	10793	0
+alignment.nex	uid46181	28217	10775	38.186	1798	149	1099	1363	581	1463	412	846	803	1574	435	450	809	705	1379	739	844	1420	176	397	0	0	0	0	0	0	10775	0
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+alignment.nex	uid49487	28217	11022	39.062	1630	206	947	1318	618	1382	350	941	980	1615	451	536	809	668	1266	770	806	1301	167	434	0	0	0	0	0	0	11022	0
+alignment.nex	uid50325	28217	10136	35.922	1960	132	1129	1240	615	1493	347	1004	1263	1516	435	556	846	554	1248	848	901	1392	198	404	0	0	0	0	0	0	10136	0
+alignment.nex	uid51371	28217	10931	38.739	1831	191	1004	1188	564	1533	342	867	914	1626	491	451	814	635	1357	721	742	1428	166	421	0	0	0	0	0	0	10931	0
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+alignment.nex	uid57951	28217	10990	38.948	1235	297	958	1144	692	1312	372	1148	1158	1467	449	627	577	475	1045	1267	728	1567	159	550	0	0	0	0	0	0	10990	0
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+alignment.nex	uid63345	28217	10839	38.413	2170	142	1041	1183	571	1476	366	963	759	1531	426	466	859	490	1459	719	906	1287	190	374	0	0	0	0	0	0	10839	0
+alignment.nex	uid65267	28217	11101	39.342	1120	156	1045	1463	712	1205	273	1310	1716	1390	404	693	596	426	937	850	696	1348	146	630	0	0	0	0	0	0	11101	0
+alignment.nex	uid65447	28217	10589	37.527	1880	145	1138	1257	607	1503	355	985	928	1506	479	480	793	538	1342	768	936	1380	195	413	0	0	0	0	0	0	10589	0
+alignment.nex	uid65785	28217	10860	38.487	1490	180	922	1269	625	1336	370	1105	978	1765	406	481	845	720	1306	784	809	1306	170	490	0	0	0	0	0	0	10860	0
+alignment.nex	uid66305	28217	11116	39.395	922	159	1012	1218	740	1102	293	1496	1896	1497	335	910	584	516	718	1196	822	1050	150	485	0	0	0	0	0	0	11116	0
+alignment.nex	uid67323	28217	10776	38.19	1636	148	1061	1320	600	1328	335	959	1078	1523	489	640	660	722	1036	951	872	1477	168	438	0	0	0	0	0	0	10776	0
+alignment.nex	uid67363	28217	10791	38.243	1580	177	1005	1242	627	1334	382	1113	1109	1565	481	635	683	744	1013	929	845	1334	173	455	0	0	0	0	0	0	10791	0
+alignment.nex	uid67391	28217	10808	38.303	1630	158	1013	1211	614	1319	381	1004	1061	1598	516	612	700	842	1007	843	905	1368	171	456	0	0	0	0	0	0	10808	0
+alignment.nex	uid68687	28217	12646	44.817	1181	155	814	1094	644	1095	326	1282	1275	1388	366	760	550	517	769	954	697	1086	138	480	0	0	0	0	0	0	12646	0
+alignment.nex	uid68745	28217	10679	37.846	1427	187	964	1202	625	1296	402	1225	1151	1633	456	724	703	747	1053	943	946	1222	163	469	0	0	0	0	0	0	10679	0
+alignment.nex	uid70791	28217	10849	38.448	1824	153	949	1246	576	1438	422	865	671	1786	399	389	878	755	1518	792	771	1316	200	420	0	0	0	0	0	0	10849	0
+alignment.nex	uid70793	28217	10492	37.183	1814	145	1014	1191	614	1447	354	1029	1136	1530	486	600	771	675	1088	868	933	1391	175	464	0	0	0	0	0	0	10492	0
+alignment.nex	uid73585	28217	10628	37.665	1780	152	1150	1125	606	1437	368	1053	1182	1400	582	592	776	580	1114	797	974	1295	190	436	0	0	0	0	0	0	10628	0

datasets/Thiergart_2014b/alignment.nex-summary.txt

@@ -0,0 +1,2 @@
+Alignment_name	No_of_taxa	Alignment_length	Total_matrix_cells	Undetermined_characters	Missing_percent	No_variable_sites	Proportion_variable_sites	Parsimony_informative_sites	Proportion_parsimony_informative	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y	B	J	Z	X	.	*	-	?
+alignment.nex	100	28217	2821700	1070273	37.93	21847	0.774	16939	0.6	162707	17031	101666	126428	63368	139156	36036	107671	112896	154596	44992	59212	74585	61267	115492	88856	86541	134809	17743	46375	0	0	0	0	0	0	1070273	0

datasets/Thiergart_2014c/README.yaml

@@ -0,0 +1,30 @@
+study:
+    reference: "Thiergart T, Landan G, Martin WF. 2014. Concatenated alignments and the case of the disappearing tree. BMC Evol. Biol. 14:266."
+    year: 2014
+    DOI: dx.doi.org/10.1186/s12862-014-0266-0
+
+dataset:
+    DOI: dx.doi.org/10.5061/dryad.06640
+    license: CC0
+    used for tree inference: yes
+    alignment:
+        ntax: 100
+        nchar: 37763
+        datatype: protein
+        partitions: 48
+    genomes:
+        mitochondrial: no
+        nuclear: no
+        chloroplast: no
+        dsDNA: no
+        ssDNA: no
+        dsRNA: no
+        ssRNA: no
+        bacterial: yes
+    timetree root age: 4290 mya
+    study root age: NA
+    study clade:
+        latin: "Procaryotae"
+        english: "Procaryote"
+        taxon ID: 2
+    notes: "This is the prokaryotic dataset with 48 genes, figure 1.A in the original paper"