0000585: Best-fit model select suggests values not allowed when constructing phylogenetic trees

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Date Submitted

Last Update

0000585

MEGA

Caption Expert

public

2017-11-01 00:28

2017-11-07 09:16

Reporter

guest

Assigned To

gstecher

Priority

normal

Severity

minor

Reproducibility

have not tried

Status

resolved

Resolution

fixed

Platform

Windows

Product Version

MEGA 11 (Graphical Interface version)

Target Version

Fixed in Version

Summary

0000585: Best-fit model select suggests values not allowed when constructing phylogenetic trees

Description

Best-fit substitution model suggests +I and +G values that cannot be entered under the "No of discrete gamma catagories" section during maximum-likelihood tree construction. Error message is "1.09 is not a valid integer value".

Steps To Reproduce

Run Best-fit substitution model on data, +G values below 2 cause this error.
Click phylogeny, select "construct/test ML tree".
Set parameters - Test of phylogeny = bootstrap
replicates = 1000
substitution type = nucleotide
model/method = any
rates among sites = gamma

gaps/missing data = use all sites (data was trimmed to shortest sequence +-530bp).
all codon positions selected
ML Heuristic method = NNI
Initial tree for ML = automatic (default NJ/BioNJ)
Branch swap filter = Moderate
No of discrete gamma categories = 1.09
Initially entering gamma = 1.09 last and pressing enter allows the run to proceed. Trying to edit this value later for a different analysis results in error message.

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First Name

Almero

Last Name

Oosthuizen

almero@nzg.ac.za

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almero@nzg.ac.za

Attached Files

MEGA7 error.png (96,635 bytes) 2017-11-01 00:28

Relationships

Notes
(0000481) paul (reporter) 1969-12-31 17:33	Suggestion is saved. Sent thank you email to user. This suggestion is closed.

(0003881) gstecher (administrator) 2017-11-07 09:16	Hi Almero, I am writing in response to the bug report you recently submitted regarding the MEGA software. To resolve the error you can do the following: Close MEGA if it is opened Navigate to the AppData directory by entering %appdata% in the Windows Explorer address bar and pressing enter This will open the c:\users\username\AppData\Roaming directory. Once in that directory, delete the folder MEGA7_7170509-x86_64 Open MEGA and run the analysis On a side note, Gamma Parameter and No of Discrete Gamma Categories are completely unrelated, so you should not enter 1.09 for No of Discrete Categories (it should be an integer value, such as 5). -- Best regards, Glen Stecher Institute for Genomics and Evolutionary Medicine igem.temple.edu

Issue History
Date Modified	Username	Field	Change
2017-11-01 00:28	guest	New Issue
2017-11-01 00:28	guest	File Added: MEGA7 error.png
2017-11-07 09:16	gstecher	Note Added: 0003881
2017-11-07 09:16	gstecher	Status	new => resolved
2017-11-07 09:16	gstecher	Resolution	open => fixed
2017-11-07 09:16	gstecher	Assigned To	=> gstecher