From c00de110376c967e089edd337c013908a1c13cb0 Mon Sep 17 00:00:00 2001
From: yangfang <506528950@qq.com>
Date: Wed, 21 Nov 2018 10:49:07 +0800
Subject: [PATCH] update doc

---
 docs/docs/faq.md      | 9 +++++++--
 docs/docs/index.md    | 2 +-
 docs/docs/tutorial.md | 4 ++--
 3 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/docs/docs/faq.md b/docs/docs/faq.md
index 12e5084..a46a0dc 100644
--- a/docs/docs/faq.md
+++ b/docs/docs/faq.md
@@ -1,6 +1,11 @@
 ### 1. What is the input of PhySpeTree?
 
-Users only need to prepare a TXT file containing [KEGG](http://www.genome.jp/kegg/catalog/org_list.html) abbreviated species names. For example, [organism_example_list](https://gitlab.com/xiaoxiaoyang/physpetools/raw/master/examples/organism_example_list.txt).
+* Users only need to prepare a TXT file containing [KEGG](http://www.genome.jp/kegg/catalog/org_list.html) abbreviated species names.
+For example, [organism_example_list](https://gitlab.com/xiaoxiaoyang/physpetools/raw/master/examples/organism_example_list.txt).
+
+* Now, PhySpeTree not only supported the user input three- or four-letter organism codes (KEGG database organism codes)
+but also the NCBI taxonomy id (for example human taxonomy id is 9606).
+You can search taxonomy id form [NCBI taxonomy database](https://www.ncbi.nlm.nih.gov/taxonomy).
 
 ### 2. How to explain PhySpeTree outputs?
 
@@ -62,5 +67,5 @@ Ribosomal protein S13                               |   K02953           |   K02
 
 ### 4. How are SSU rRAN created?
 
-The SSU rRAN sequences are created from the [SILVA](<https://www.arb-silva.de/>) database (123.1 release). Sequences haven been truncated, which means unaligned nucleotides are removed.
+The SSU rRAN sequences are created from the [SILVA](<https://www.arb-silva.de/>) database (Release 132, Released: 13.12.2017). Sequences haven been truncated, which means unaligned nucleotides are removed.
 
diff --git a/docs/docs/index.md b/docs/docs/index.md
index 261f385..c6a5e36 100644
--- a/docs/docs/index.md
+++ b/docs/docs/index.md
@@ -1,7 +1,7 @@
 
 # PhySpeTree: automatically reconstructing phylogenetic species tree
 
-**PhySpeTree is implemented in Python language, designed for Linux systems.**
+**PhySpeTree is implemented in Python language (supports Python2.7+ and Python3+), designed for Linux systems.**
 
 ## Introduction
 
diff --git a/docs/docs/tutorial.md b/docs/docs/tutorial.md
index 8d19f9d..fc07757 100644
--- a/docs/docs/tutorial.md
+++ b/docs/docs/tutorial.md
@@ -727,7 +727,7 @@ Status: Downloaded newer image for yangfangs/physpetree:v0.3.4
 REPOSITORY             TAG                 IMAGE ID            CREATED             SIZE
 yangfangs/physpetree   v0.3.4              ebcdaff79f7c        41 hours ago        683MB
 ```
-### 3. run PhySpeTree image
+### 4. run PhySpeTree image
 
 * You need to run docker with an interactive bash and mount it in a local directory with a working directory in docker (PhySpeTree_work_dir).
 
@@ -735,7 +735,7 @@ yangfangs/physpetree   v0.3.4              ebcdaff79f7c        41 hours ago
 [yangfang@localhost ~]$ docker run -it -v /home/yangfang/work_dir/:/PhySpeTree_work_dir yangfangs/physpetree:v0.3.4 bash
 root@2d68776ac9ad:/PhySpeTree_work_dir#
 ```
-### 3. Run PhySpeTree in Docker
+### 5. Run PhySpeTree in Docker
 
 * Download test file