initial commit

README.md

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 tree-of-trees
 =============
 
-Megatree construction from component trees, associated with phylomatic
+Megatree construction from component trees, associated with phylomatic
+
+## Directories:
+
+ * `ages/` : `phylocom bladj` ages files
+ * `doc/` : documentation
+ * `megatrees/` : assembled megatrees
+ * `megatrees_other/` : useful megatrees from other projects
+ * `pmmd/` : ‘phylomatic metadata’ XML schema, used for documenting
+   phylogenies
+ * `tools/` : tools for manipulating and assembling trees
+ * `trees/` : contributed component trees
+ * `trees_not-yet-checked/` : contributed component trees, not yet
+   checked for XML, naming conventions and Newick validity
+

ages/euphyllophyte_wikstrom2001.ages

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+euphyllophyte	400.0
+seedplants	325.0
+angiosperm	179.0
+nym2ast	171.0
+aus2ast	165.0
+poales_to_asterales		161.0
+monocotneudicot	161.0
+eudicot	147.0
+bux2ast	137.0
+coreeudicot	127.0
+subrosid	121.0
+eurosid1	98.0
+malpighiales	81.0
+flacourtiaceae	23.0
+salicaceae	20.0
+passifloraceae	26.0
+rhizophoraceae	9.0
+malpighiaceae	32.0
+picrodendraceae	38.0
+chrysobalanaceae	8.0
+linaceae	33.0
+oxalidales	77.0
+oxalidaceae	43.0
+cunoniaceae	42.0
+elaeocarpaceae	59.0
+celastrales	42.0
+celastraceae	34.0
+parnassiaceae	19.0
+fabales	79.0
+fabaceae	56.0
+polygalaceae	28.0
+fagales	61.0
+betulaceae	19.0
+juglandaceae	6.0
+fagaceae	34.0
+cucurbitales	65.0
+cucurbitaceae	20.0
+rosales	76.0
+elaeagnaceae	13.0
+rhamnaceae	55.0
+urticaceae	22.0
+moraceae	23.0
+rosaceae	47.0
+zygophyllales	70.0
+myrtales	88.0
+onagraceae	20.0
+lythraceae	37.0
+combretaceae	27.0
+eurosid2	95.0
+sapindales	61.0
+sapindaceae	36.0
+meliaceae	30.0
+rutaceae	39.0
+bursa2anaca	51.0
+malvales	68.0
+thymelaeaceae	26.0
+malvaceae	34.0
+brassicales	79.0
+acaniaceae	31.0
+brassicaceae	24.0
+limnanthaceae	9.0
+crossosomatales	62.0
+geraniales	92.0
+geraniaceae	38.0
+vitaceae	92.0
+saxifragales	111.0
+altingiaceae	56.0
+crassulaceae	41.0
+haloragaceae	17.0
+saxifragaceae	51.0
+hamamelidaceae	104.0
+asterid	117.0
+euasterid2	107.0
+dipsacales	81.0
+dipsacaceae	10.0
+adoxaceae	57.0
+apiales	69.0
+apiaceae	33.0
+araliaceae	26.0
+pittosporaceae	14.0
+asterales	90.0
+asteraceae	44.0
+menyanthaceae	51.0
+campanulaceae	33.0
+aquifoliales	97.0
+icacinaceae	65.0
+euasterid1	107.0
+lamiales	63.0
+acanthaceae	31.0
+lamiaceae	23.0
+bignoniaceae	38.0
+verbenaceae	20.0
+gesneriaceae	38.0
+utriculariaceae	28.0
+oleaceae	47.0
+boraginaceae	59.0
+solanales	78.0
+convolvulaceae	20.0
+solanaceae	41.0
+gentianales	71.0
+apocynaceae	18.0
+rubiaceae	56.0
+garryales	93.0
+ericales	100.0
+ericaceae	12.0
+styracaceae	45.0
+ternstroemiaceae	54.0
+polemoniaceae	35.0
+lecythidaceae	65.0
+cornales	101.0
+cornaceae	64.0
+nyssaceae	43.0
+loasaceae	67.0
+hydrangeaceae	78.0
+caryophyllales	84.0
+polygonaceae	28.0
+plumbaginaceae	27.0
+nyctaginaceae	13.0
+amaranthaceae	19.0
+dilleniaceae	52.0
+santalales	69.0
+loranthaceae	26.0
+santalaceae	37.0
+trochodendraceae	106.0
+buxaceae	97.0
+sabiaceae	129.0
+proteales	135.0
+proteaceae	47.0
+ranunculales	140.0
+lardizabalaceae	77.0
+circaeasteraceae	54.0
+berberidaceae	44.0
+ranunculaceae	65.0
+menispermaceae	53.0
+papaveraceae	112.0
+asparagales	107.0
+poales	72.0
+bromeliaceae	33.0
+cyperaceae	16.0
+poaceae	12.0
+zingiberales	62.0
+marantaceae	23.0
+costaceae	27.0
+zingiberaceae	10.0
+strelitziaceae	29.0
+musaceae	50.0
+commelinales	68.0
+arecaceae	73.0
+convallariaceae	27.0
+hyacinthaceae	29.0
+amaryllidaceae	28.0
+iridaceae	32.0
+orchidaceae	26.0
+liliales	96.0
+liliaceae	48.0
+pandanaceae	88.0
+cyclanthaceae	45.0
+dioscoreales	95.0
+alismatales	124.0
+araceae	98.0
+magnoliales	113.0
+annonaceae	26.0
+magnoliaceae	70.0
+myristicaceae	23.0
+canellales	99.0
+winteraceae	42.0
+canellaceae	17.0
+laurales	111.0
+calycanthaceae	52.0
+lauraceae	34.0
+monimiaceae	71.0
+piperales	132.0
+aristolochiaceae	108.0
+saururaceae	75.0
+piperaceae	43.0
+chloranthaceae	132.0
+nymphaeaceae	132.0

doc/FAQ.md

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+# FAQ for Tree-of-trees/Phylomatic database
+
+## Q: Why won't the megatrees (e.g., R20081027.new) open in TreeViewX?
+
+A: The phylomatic database allows single daughter nodes in Newick:
+((A,B)C)D which are also allowed by the Newick standard.  TreeView can
+also handle these, but seems not to like it when the files are large.
+The single daughter nodes can be cleaned out using phylocom, e.g.:
+
+      $ phylocom phylocom cleanphy -e -f R20081027.new > clean.new
+
+The resulting file will open in TreeView.  I have found that ATV
+can open the files directly.
+
+## Q: Are the XML files valid?
+
+A: Cam regularly runs: jing -c pmmd/pmmd.rnc trees/*.xml
+But... the XML files are hand coded, so errors may creep in once in a while.
+