0006157: Ancestral reconstruction error involving indels

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0006157

MEGA

Calculation Error

public

2023-10-12 10:53

Reporter

guest

Assigned To

Priority

normal

Severity

minor

Reproducibility

have not tried

Status

new

Resolution

open

Platform

Windows

Product Version

MEGA 11 (Graphical Interface version)

Target Version

Fixed in Version

Summary

0006157: Ancestral reconstruction error involving indels

Description

When inferring ancestral sequences from an alignment in MEGA11, if any sequence in the alignment has an insertion relative to the other sequences in the alignment, all inferred ancestors will contain that insertion, regardless of their phylogenetic position. Additionally, if the alignment contains a gap, the gap will be filled in with a continuous stretch of the same base, typically a stretch of adenines, although I have also seen polyC inserts as well.

Steps To Reproduce

1) Create sequence alignment with at least one sequence that has an insertion relative to the other sequences in the file. Example uploaded: 21-05-17_env_musc_gap.fas
2) Create maximum likelihood tree using Tamura-Nei model.
3) Use ML tree from step two as guide tree for ancestral state reconstruction.
4) Export most probable ancestral sequences as either text file or Excel file.

Alternately, to reproduce the second type of bug, create an alignment file with an unfilled gap, continue to step 2. 21-05-17_env_musc_gap.fas has both indels and an inserted gap of this type, at position 63 in the alignment.

Additional Information

The bug appears specific to MEGA11, as I have not had this problem with MEGA X.

Issue History
Date Modified	Username	Field	Change
2023-10-12 10:53	guest	New Issue
2023-10-12 10:53	guest	File Added: 21-05-17_env_musc_gap.fas

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