最近在完成一项任务的时候要利用cdhit序列聚类软件对几万条的序列文件进行聚类，基本摸清了用法，在此记录一下，并在此感谢肥肥的帮助
经历这件事，我吸取了教训，就是想要摸清一个软件的全部用法，不应该只是凭着在google中搜到的几个帖子就下定论，即使别人的帖子是很新的，但是也是各取所需的结果，并不一定会把整个软件的全部功能都在一张帖子里面说尽。因此最重要的就是 研读 User's guide 和 软件的github.com上面的wiki 里面的 user's guide。后者往往比前者要新，因为时常会更新。
Cdhit详细说明了每一个参数的使用，以下挑选了重要的来说明：
- -G
use global sequence identity, default 1。 - -S
length difference cutoff in amino acid, default 999999 if set to 60, the length difference between the shorter sequences and the representative of the cluster can not be bigger than 60。 - -aL
alignment coverage for the longer sequence, default 0.0。if set to 0.9, the alignment must covers 90% of the sequence。 - -aS
alignment coverage for the shorter sequence, default 0.0。if set to 0.9, the alignment must covers 90% of the sequence。 - -U
maximum unmatched length, default 99999999 if set to 10, the unmatched region (excluding leading and tailing gaps) must not be more than 10 bases。 - -g
1 or 0, default 0 。by cd-hit's default algorithm, a sequence is clustered to the first
cluster that meet the threshold (fast cluster). If set to 1, the program will cluster it into the most similar cluster that meet the threshold (accurate but slow mode)。 - -uL
maximum unmatched percentage for the longer sequence, default 1.0。if set to 0.1, the unmatched region (excluding leading and tailing gaps) must not be more than 10% of the sequence - -uS
maximum unmatched percentage for the shorter sequence, default 1.0。if set to 0.1, the unmatched region (excluding leading and tailing gaps) must not be more than 10% of the sequence
所以最后我实际运行的命令是：
cdhit -i in.fasta -o out.fasta -d 30 -G 1 -M 16000 -T 20 -S 2 -U 2 -g 1 -aL 0.95 -aS 1
因为没有看最新的github wiki上面的 guide 所以不知道 -uL 和 -uS参数，不过也能基本上满足我的要求
最好应该是下面的命令：
cdhit -i in.fasta -o out.fasta -d 30 -G 1 -M 16000 -T 20 -uL 0.05 -S 2 -U 2 -g 1 -aL 0.95 -aS 1
以上！
