MBV4410/9410 Fall 2017

Bioinformatics for Molecular Biology

JalView (alignment software)

Today’s program

• Genome browsers• Exercise• Jalview• Working with sequence data• After lunch: Exercises

Software for viewing and analysing sequences

• Lots of programs – should be free, but not always…• Visualization• Multiple sequence alignment programs (Mafft, Muscle, T-

Cofee, Clustal…)• Phylogenetic reconstruction (RAxML, Phylobayes…)• Other (population size, mutation rates, substitution patterns,

selection tests…)

Mesquite (http://mesquiteproject.wikispaces.com/)

MEGA (http://www.megasoftware.net/)

Geneious (https://www.geneious.com/)

JalView (http://www.jalview.org/)

Sample file