A Tool for Refining a Multiple Alignment on a Phylogenetic Tree
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We tested the performance of TreeRefiner on alignments generated by MLAGAN, MAVID and TBA
using 100kb long sequences which were generated by Rose. For each of the four combinations of
the parameters (two different trees and two different mutation rates), we have provided the
unaligned sequences (generated by Rose), the true alignment (generated by Rose), the alignments
computed by MLAGAN, MAVID, TBA and the TreeRefiner refinements of the these alignments using four
different radii. Click on the links below to view the appropriate alignments
((Human Baboo)(Mouse Rat)) (unaligned sequences)
The True Alignment (generated by Rose)
((Human Baboo)(Mouse Rat)) + Higher Mutation Rate (unaligned sequences)
The True Alignment (generated by Rose)
| MLAGAN |
MAVID |
TBA |
| TR radius 1 |
TR radius 1 |
TR radius 1 |
| TR radius 2 |
TR radius 2 |
TR radius 2 |
| TR radius 4 |
TR radius 4 |
TR radius 4 |
| TR radius 8 |
TR radius 8 |
TR radius 8 |
(((Human Baboo)(Mouse Rat))((cow pig)(cat dog))) (unaligned sequences)
The True Alignment (generated by Rose)
| MLAGAN |
MAVID |
TBA |
| TR radius 1 |
TR radius 1 |
TR radius 1 |
| TR radius 2 |
TR radius 2 |
TR radius 2 |
| TR radius 4 |
TR radius 4 |
TR radius 4 |
| TR radius 8 |
TR radius 8 |
TR radius 8 |
(((Human Baboo)(Mouse Rat))((cow pig)(cat dog))) + Higher Mutation Rate (unaligned sequences)
The true alignment (generated by Rose)
| MLAGAN |
MAVID |
TBA |
| TR radius 1 |
TR radius 1 |
TR radius 1 |
| TR radius 2 |
TR radius 2 |
TR radius 2 |
| TR radius 4 |
TR radius 4 |
TR radius 4 |
| TR radius 8 |
TR radius 8 |
TR radius 8 |