XCED for Linux/x86
A Tool for Multiple Sequence Alignment and Phylogenetic Tree Inference
xced-8a.3.93-rh80_slink.i386.rpm (built on Red Hat Linux 8.0, updated at 2003/05/06)
xced-8a.3.93-rh73_slink.i386.rpm (built on Red Hat Linux 7.3, updated at 2003/05/06)
These packages include a modified version of the
protml
program (Adachi and Hasegawa 1996).
The following are not necessary but preferred.
- NJPLOT (Perrière and Gouy 1996) http://pbil.univ-lyon1.fr/software/njplot.html
- FASTA version 3.0 (Pearson and Lipman 1988) ftp://ftp.virginia.edu/pub/fasta/fasta30t63.shar.Z
- Ruby ftp://ftp.redhat.com:/pub/redhat/linux/ (Download and install the proper package for your system.)
- Netscape or another web browser
# rpm -Uvh xced-8a.?.?-rh73_slink.i386.rpm
If you have fasta3 and/or njplot, put them into your command path.
If you do not have Netscape, you need to set the XCED_BROWSER environment
variable to your favorite browser to get sequence data from
NCBI and other information:
% setenv XCED_BROWSER /usr/bin/opera
or
% setenv XCED_BROWSER 'kterm -e w3m'
The type (protein or DNA) of input sequences is automatically recognized.
Aligning sequences
- Select 'Distance/Initialize/Sextet' from the menu. A distance matrix for constructing a guide tree is calculated.
- Select the sequences to be aligned with the left button of your mouse. You can also select all sequences by Ctrl+LeftButton.
-
Select 'Align/Progressive' and click the OK button of the 'Progressive Alignment' dialog.
- The resulting alignment may be improved by 'Align/Iterative Refinement' or your eyes.
Inferring a molecular phylogenetic tree by the neighbor-joining (NJ) method (Saitou and Nei 1987)
- Select 'Edit/Tree-Inference Regions/Automatic' and click the OK button to select unambiguously aligned positions to be subjected to phylogeny inference. The selected positions are indicated with the 'O' marks above the alignment.
- Select 'View/NJ Tree' and click the OK button at the 'Phylogenetic Tree' dialog. A distance matrix is estimated by the ML method assuming the JTT model without among-site rate heterogeneity by default for amino acid sequences. The evolutionary model can be switched to the JTT gamma model or the Poisson model at the 'Phylogenetic Tree' dialog. A bootstrap analysis is carried out if the 'Bootstrap' option is turned on.
