Merge 51b13dd into f0ab25a

README.rst

@@ -1,31 +1,15 @@
-hybrid_tree
-===========
+ghost-tree
+==========
 
 |Build Status| |Coverage Status|
 
-<p>
-This is a two genetic marker phylogenetic tree: hybrid tree
-
-Installation instructions:<p>
-
-For BOTH scripts, you need 3 input files:<p>
-  1)repset of ITS seqs<p>
-  2)taxonomy file<p>
-  --above are in Google Drive (will share)<p>
-  3)Silva 18S file:<p>
-  http://www.arb-silva.de/fileadmin/silva_databases/release_115/Exports/SSURef_NR99_115_tax_silva_full_align_trunc.fasta.tgz
-  (very large, full alignment, non-redundant SSU, has ALL eukaryotes which is unnecessary)
-<p>
-
-There are two scripts, one relies on Qiime (make_hybrid_tree.py) and the other one (skbio_hybrid_tree_wip.py) uses skbio with FastTree and Muscle installed locally
-
-"python make_hybrid_tree.py" can be run in command line in QIIME in the working directory where your 3 files are; It uses Muscle and Fasttree from within QIIME (and other Qiime scripts)
-<p>
-<p>
-skbio_hybrid_tree_wip.py is the transition away from Qiime dependency; CHANGE input files at the bottom of python script & change directory of FastTree and Muscle (you must download and install locally)
-<p>
-<p>
+ghost-tree is a bioinformatics tool that combines sequence data from two
+genetic marker databases into one phylogenetic tree that can be used for
+diversity analyses. One database is used as a backbone or scaffold because it
+provides better phylogeny across all phyla, and the other database provides
+finer taxonomic resolution.
 
+This project is currently under active development.
 
 
 .. |Build Status| image:: https://travis-ci.org/JTFouquier/ghost-tree.svg?branch=master

legacy/README.html

@@ -0,0 +1,22 @@
+<p>
+This is a two genetic marker phylogenetic tree: hybrid tree
+
+Installation instructions:<p>
+
+For BOTH scripts, you need 3 input files:<p>
+  1)repset of ITS seqs<p>
+  2)taxonomy file<p>
+  --above are in Google Drive (will share)<p>
+  3)Silva 18S file:<p>
+  http://www.arb-silva.de/fileadmin/silva_databases/release_115/Exports/SSURef_NR99_115_tax_silva_full_align_trunc.fasta.tgz
+  (very large, full alignment, non-redundant SSU, has ALL eukaryotes which is unnecessary)
+<p>
+
+There are two scripts, one relies on Qiime (make_hybrid_tree.py) and the other one (skbio_hybrid_tree_wip.py) uses skbio with FastTree and Muscle installed locally
+
+"python make_hybrid_tree.py" can be run in command line in QIIME in the working directory where your 3 files are; It uses Muscle and Fasttree from within QIIME (and other Qiime scripts)
+<p>
+<p>
+skbio_hybrid_tree_wip.py is the transition away from Qiime dependency; CHANGE input files at the bottom of python script & change directory of FastTree and Muscle (you must download and install locally)
+<p>
+<p>