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

Phylogenetic Trees Linear
Building Phylogenetic Trees

Learn how to learn how to align sequences and build a phylogenetic tree

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Pairwise Alignment

Learn how to align pairs of DNA and protein sequences using dotplots and alignment algorithms.

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Aligning Bacterial Genomes with Mauve

Learn how to align bacterial genomes using the Mauve plugin for Geneious Prime.

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Prime - BLAST
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.

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