MantisBT - MEGA
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IDProjectCategoryView StatusDate SubmittedLast Update
0000181MEGAAlignment Explorerpublic2016-05-27 17:062023-04-14 00:50
Reporterguest 
Assigned To 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusnewResolutionopen 
PlatformMacOSOS XOS Version10.11
Product VersionMEGA-CC 11 (command line version) 
Target VersionFixed in Version 
First Namerex
Last Namemalmstrom
Emailrrmalmstrom@lbl.gov
Confirm Emailrrmalmstrom@lbl.gov
Summary0000181: clustal nuc alignment not generating proper alignment
DescriptionThere is a huge discrepancy in the alignment when using megacc and mega 6.0 through graphic interface when aligning same input file and keep all other parameters the same.

megacc appears not to attempt alignment. E.g. output is generated instantly and there are no gaps in the .meg output file.

Alignment of same fasta file using graphic interface on Mega 6.0 produces proper alignment with gaps inserted.

Steps To ReproduceHere is example of .mao for clustal alignment of non-coding DNA:


; Please do not edit this file! If this file is modified, results are unpredictable.
; Instead of modifying this file, simply create a new MEGA Analysis Options file by using the MEGA Prototyper.
[ MEGAinfo ]
ver = 7151208-x86_64 Mac OS
[ DataSettings ]
datatype = snNucleotide
containsCodingNuc = False
missingBaseSymbol = ?
identicalBaseSymbol = .
gapSymbol = -
[ ProcessTypes ]
ppAlign = true
ppClustalW = true
[ AnalysisSettings ]
Pairwise Alignment = ====================
DNAPWGapOpeningPenalty = 15.00
DNAPWGapExtensionPenalty = 6.66
Multiple Alignment = ====================
DNAMAGapOpeningPenalty = 15.00
DNAMAGapExtensionPenalty = 6.66
Global Options = ====================
DNA Weight Matrix = IUB
TransitionWeightNEdit = 0.50
UseNegativeMatrix = OFF
DelayDivergentCutoff = 30
KeepPredefinedGaps = False
Additional InformationI've attached a copy of the input fasta file.
TagsNo tags attached.
Relationships
Attached Files? target.16S.25m.fasta copy (24,144) 2016-05-27 17:06
https://megasoftware.net/mantis_bt/
Issue History
Date ModifiedUsernameFieldChange
2016-05-27 17:06guestNew Issue
2016-05-27 17:06guestFile Added: target.16S.25m.fasta copy
2023-01-13 08:01guestNote Added: 0005961
2023-01-13 08:05guestNote Added: 0005962
2023-01-13 10:40guestNote Added: 0005963
2023-01-13 13:11guestNote Added: 0005964
2023-01-13 14:52guestNote Added: 0005965
2023-01-13 14:54guestNote Added: 0005966
2023-01-13 15:29guestNote Added: 0005967
2023-01-13 16:27guestNote Added: 0005968
2023-01-13 18:44guestNote Added: 0005969
2023-04-14 00:50guestNote Added: 0006318

Notes
(0000101)
Nikita Vikhrev   
1969-12-31 17:33   
Fixed.
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