Each download we provide is subject to periodical scanning, but we strongly recommend you check the package for viruses on your side before running the installation. Clustalx is distributed free of charge. The download version of clustalx is 2.1. The package you are about to download is authentic and was not repacked or modified in any way by us.
6.891 Laboratory 2 Tools
- Knoppix Molevolution CD-rom (PCÕs only so far, sorry): boot from CD (using Bios). Contains: ClustalX, TreeView, PAML, LAMARC, PAUP*, others.
- For dN/dS calculations
- SNAP:http://hcv.lanl.gov/content/hcv-db/SNAP/SNAP.html
- (optional on PC): download DnaSP from http://www.ub.es/dnasp/
- For alignments/format conversion: ClustalX
- Download for Mac from website:
![Clustalx Download For Mac Clustalx Download For Mac](http://www.cbs.dtu.dk/dtucourse/27611spring2009/exercises/ExMul+Phyl/ClustalX_mac.png)
http://web.mit.edu/6.891/www/Clustalx-1.83-MacOS-X.tar
- For PC, use Molix Cd-rom: clustalx
- (or download yourself on PC): http://web.mit.edu/6.891/www/clustalx1.83.XP.zip
- General web page at : http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html
- For simple format conversions (fasta/clustalw/table/mega), if you donÕt want to use ClustalX, you can use the web form at:
http://hcv.lanl.gov/content/hcv-db/SEQCONVERT/seqconvert.html
- For advanced dN/dS analysis using likelihoods, or PAML
- Download for Mac from website: http://web.mit.edu/6.891/www/paml3.14.tar.gz
See instructions/docs at http://abacus.gene.ucl.ac.uk/software/paml.html
- For PC, useMolix Cd-rom, codeml
- Or download .exe file for PC:http://web.mit.edu/6.891/www/paml3.14.tar.gz
- For Josh PlotkinÕs volatility analysis
- Server site: http://volatility.cgr.harvard.edu/cgi-bin/volatility.pl
- For coalescent animation/tests, see:
![Clustalx Clustalx](/uploads/1/2/5/7/125772118/933143108.png)
http://www.coalescent.dk/ and click on ÒWright-FisherÓ animator or ÒHudsonÓ animator
- For drawing phyogenetic trees after alignment: use TreeView from the Cd-rom: tv
Data sources
- Yeast alignments downloadable directly http://web.mit.edu/6.891/www/genes.tar.gz(11mb compressed, 64mb uncompressed; all alignments from chromosome 2: http://web.mit.edu/6.891/www/chr2.tar.gz(813kb compressed, 9mb uncompressed)
- Yeast database at Broad Institute: http://www.broad.mit.edu/annotation/fungi/comp_yeasts/index.html
- Test data for ÔwarmupÕ sections of the lab: Kreitman drosophila data; human/primate globin data, etc. will all be on http://web.mit.edu/6.891/www/as needed. (The laboratory will include links to these files)
Downloading clustalx 2.1
Clustal X is a windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analysing the results.
The sequence alignment is displayed in a window on the screen. A versatile coloring scheme has been incorporated allowing you to highlight conserved features in the alignment. The pull-down menus at the top of the window allow you to select all the options required for traditional multiple sequence and profile alignment.
You can cut-and-paste sequences to change the order of the alignment; you can select a subset of sequences to be aligned; you can select a sub-range of the alignment to be realigned and inserted back into the original alignment.
Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted.
To start download, click the following link:
The sequence alignment is displayed in a window on the screen. A versatile coloring scheme has been incorporated allowing you to highlight conserved features in the alignment. The pull-down menus at the top of the window allow you to select all the options required for traditional multiple sequence and profile alignment.
You can cut-and-paste sequences to change the order of the alignment; you can select a subset of sequences to be aligned; you can select a sub-range of the alignment to be realigned and inserted back into the original alignment.
Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted.
To start download, click the following link:
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