LEARN GENEIOUS
Alignment and Tree Building
Watch videos and complete tutorials to learn how to do multiple alignments, bacterial genome alignments and build phylogenetic trees.
Intro to Multiple Alignments
INSIDE THE VIDEO
Multiple alignments is used to assess levels of homology among a group of sequences and is necessary before you can construct a phylogeny.
LEARN HOW TO:
- Choose an alignment algorithm
- Perform a multiple sequence alignment using MUSCLE
- View the alignment
Introduction to Phylogenetic Trees
INSIDE THE VIDEO
Basic steps to build a tree and manipulate the tree viewer in Geneious Prime
LEARN HOW TO:
- Perform a multiple alignment
- Choose your tree builder and parameters
- Build a phylogenetic tree
- View and manipulate your tree
Pairwise Alignments – Dot Plots
INSIDE THE VIDEO
View the regions of similarity between pairs of sequences using a dot plot
LEARN HOW TO:
- View and customize the dot plot
- View sequence inversions
- View repeating patterns the sequence
Pairwise Alignment of DNA Sequences
INSIDE THE VIDEO
Perform pairwise alignment of two related sequences to determine homology.
LEARN HOW TO:
- Perform a pairwise alignment
- Choose an alignment algorithm
- Optimize and refine your alignments
How To Align Whole Genomes with Mauve
INSIDE THE VIDEO
Align bacterial genomes using the Mauve plugin for Geneious Prime
LEARN HOW TO:
- Align complete bacterial genomes with progressiveMauve
How To Align Draft Genomes with the Mauve Contig Mover
INSIDE THE VIDEO
Align bacterial genomes using the Mauve plugin in Geneious Prime
LEARN HOW TO:
- Order draft genomes against a reference sequence with the Mauve contig mover
How To Convert a Mauve Alignment to a Standard Alignment
INSIDE THE VIDEO
Convert a Mauve alignment into a standard alignment for use in downstream applications including phylogenetic tree building
LEARN HOW TO:
- Convert a Mauve alignment into a standard alignment
TUTORIALS
Building Phylogenetic Trees
Learn how to learn how to align sequences and build a phylogenetic tree
Pairwise Alignment
Learn how to align pairs of DNA and protein sequences using dotplots and alignment algorithms.
Aligning Bacterial Genomes with Mauve
Learn how to align bacterial genomes using the Mauve plugin for Geneious Prime.
Case Study – Plant Molecular Evolution
Annotate plant DNA sequences using BLAST and multiple alignment, then learn how to read a phylogenetic tree to explore genetic distance.