Private division

1. making private divisions

Users in account mode can make their own division, which is called private division, to analyze their own data. The followings are ways to make a private division. Users can also combine two more more processes.

1.1. from map information

You can make a division by extracting partial data from master database by use of Map Viewer.

1.2. from phylogenetic tree

You can make a division by extracting partial data from master database by use of Tree Viewer.

1.3. uploading a local file

If you click 'make a division by uploading a data file' link in 'access to private division' page, a file uploading form is displayed. You can set a data set by uploading a local file or by copying & pasting it to the text field. FASTA, GenBank/DDBJ and EMBL formats are acceptable. After typing division name to be made and selecting molecular type (nucleic or amino acids), you can amke a new divisin by clicking 'upload' button.

1.4. copying another division

If you click 'copying an existing division' link in 'access to private division' page, a list of divisions which can be copied is displayed. After choosing one and typing a new division name, you can copy it by clicking 'copy' button.

1.5. merging divisions

If you click 'merge' link in 'access to private division' page, a list of private divisions is displayed. After choosing two or more and typing a new division name, you can merge them by clicking 'go' button.
If there are duplications of IDs, an editor page is displayed. In this page, you need to change IDs or remove entries until the duplications are disappeared.

2. analyses of private divisions

In analyses of data in private divisions, users can choose various options and parameters.

2.1. available parameters

multiple alignment (CLUSTALW)
- default : accurate but slow
- quicktree : fast but approximate
genetic distance calculation for nuclecic acid sequences
- 1 parameter method by Jukes & Cantor
- 2 parameters method by Kimura
- 3 parameters method by Kimura
- 4 parameters method by Takatata & Kimura
- method by Tajima & Nei
- 6 parameter method by Gojobori
- gamma distance method with 1 parameter
- gamma distance method with 2 parameters
genetic distance calculation for amino acid sequences
- Zuckerkandl & Pauling method
- Kimura method
phylogenetic tree calculation
- UPGMA method
- NJ method
bootstrap re-sampling
- number of re-sampling can be set

2.2. status of analysis

You can refer the status of each private division by clicking 'show status of divisions' link in 'access to private divisions' page. You can confirm the reasons in this page if your analysis jobs stops abnormally.