0001828: treating missing data and gaps in multigene phylogenetics

View Issue Details [ Jump to Notes ]

[ Issue History ] [ Print ]

Project

Category

View Status

Date Submitted

Last Update

0001828

MEGA

Calculation Error

public

2020-03-08 10:54

2020-03-09 07:26

Reporter

guest

Assigned To

gstecher

Priority

normal

Severity

minor

Reproducibility

have not tried

Status

resolved

Resolution

no change required

Platform

Windows

Product Version

MEGA 11 (Graphical Interface version)

Target Version

Fixed in Version

Summary

0001828: treating missing data and gaps in multigene phylogenetics

Description

Report bugs or other issues regarding the MEGA software
I got a trouble to solve treating missing data/ gaps in multigene phylogenetic tree with Neighbor-joining tree. My data can use Maximum likelihood tree and Maximum parsimony tree test with only "use all sites" option, but I do not know which method MEGA program used to treat missing data and gaps. I only see the infomation about "Pairwise-Deletion" and "Complete-Deletion", not "use all sites" option. How is it different to other programs like RAxML and MrBayes? Thank you.

Additional Information

I also tested another published data from a paper "A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes". and met similar problems.

Tags

No tags attached.

Attach Tags

(Separate by ",")

First Name

Son

Last Name

Hoang Kim

Hoangkimsonbio@gmail.com

Confirm Email

Hoangkimsonbio@gmail.com

Attached Files

5 genes SSU LSU TEF RPB1 RPB2 2.fasta (388,514 bytes) 2020-03-08 10:54

Relationships

Notes
(0004418) gstecher (administrator) 2020-03-09 07:26	Hi Son, I am writing in response to your question regarding the MEGA software. Neighbor-Joining is a distance-based method so some options such as gap treatment are different than for Maximimum Likelhood and Maximium Parsimony analyses. The 'use all sites' option is not available for distance-based methods as it is not valid for the method. -- Best regards, Glen Stecher Institute for Genomics and Evolutionary Medicine igem.temple.edu

Issue History
Date Modified	Username	Field	Change
1969-12-31 17:33	user19	Note Added: 0001610
1969-12-31 17:33	user19	Status	new => assigned
1969-12-31 17:33	user19	Assigned To	=> user19
1969-12-31 17:33	user19	Note Added: 0001684
1969-12-31 17:33	user19	Note Added: 0001685
1969-12-31 17:33	user19	Note Added: 0001686
1969-12-31 17:33	user19	Note Edited: 0001686
1969-12-31 17:33	user19	Status	assigned => closed
1969-12-31 17:33	user19	Resolution	open => fixed
2020-03-08 10:54	guest	New Issue
2020-03-08 10:54	guest	File Added: 5 genes SSU LSU TEF RPB1 RPB2 2.fasta
2020-03-09 07:25	gstecher	Note Deleted: 0001610
2020-03-09 07:25	gstecher	Note Deleted: 0001684
2020-03-09 07:25	gstecher	Note Deleted: 0001685
2020-03-09 07:26	gstecher	Note Deleted: 0001686
2020-03-09 07:26	gstecher	Note Added: 0004418
2020-03-09 07:26	gstecher	Status	new => resolved
2020-03-09 07:26	gstecher	Resolution	open => no change required
2020-03-09 07:26	gstecher	Assigned To	=> gstecher