Backup of Conservation Genetics of Mangroves/Seminars/Data Analysis(No. 5)

Data Analysis †

1. Sequence data editing by Sequence Scanner Software v1.0
Using this software, you can view, edit, print and export sequence text data generated by the Applied Biosystems Genetic Analyzers. This software also generates graphically expressive reports on results.
2. MEGA4 is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.

3. Peak Scanner™ Software v1.0
Use this free software to perform DNA fragment analysis; separate a mixture of DNA fragments according to their sizes, provide a profile of the separation, and precisely calculate the sizes of the fragments. The software allows you to view, edit, analyze, print, and export fragment analysis data generated using the Applied Biosystems Genetic Analyzers.

4. Notepad++ is a free (as in "free speech" and also as in "free beer") source code editor and Notepad replacement that supports several languages. Running in the MS Windows environment, its use is governed by GPL License.
Regular expression can be used in search/replace. See the explanation of Regular Expression in http://www.scintilla.org/SciTERegEx.html

5. Bioedit
Useful software to edit sequences, align, and analyze data. You can edit sequence data (electropherogram) generated by ABI sequencer.

6. Jedit is a mature programmer's text editor with hundreds (counting the time developing plugins) of person-years of development behind it.

Sometimes, you want to download sequences that are published in a paper. For example, look at this paper: Ted R. Schultz and Sean G. Brady. 2008. PNAS. 105(14): 5435-5440., "Major evolutionary transitions in ant agriculture"
What you should do to download GenBank is preparing list of accession numbers
In the supplement information, Table S2, accession numbers are listed.
To obtain these sequence from GenBank, you need to prepare, comma delimited accession numbers
```
Accession number 1, Accession number 2, ....
```
- To do this, follow the work flow in the text editor
  - Copy data from the Table S2
Using Notepad++, do search/replace using regular expression
- At first, repeated appeared same pattern will be replaced (spaces and dots should be replaced into other characters
```
no seq → no_seq
cf.  → cf_
```
- multiple white spaces to something tab
```
 +  → \t
↑here is a <white space>
```
- Copy all and paste it to Excel, then you will get the list of accession numbers in column
- Copy a column and paste it to Notepad++
- replace the end of line to comma
```
 \n → ,
```