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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 X 
Product VersionMEGA-CC 11 (command line version) 
Target VersionFixed in Version 
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.
Attach Tags (Separate by ",")
First Namerex
Last Namemalmstrom
Emailrrmalmstrom@lbl.gov
Confirm Emailrrmalmstrom@lbl.gov
Attached Files? file icon target.16S.25m.fasta copy (24,144 bytes) 2016-05-27 17:06

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

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- Issue History
Date Modified Username Field Change
2016-05-27 17:06 guest New Issue
2016-05-27 17:06 guest File Added: target.16S.25m.fasta copy
2023-01-13 08:01 guest Note Added: 0005961
2023-01-13 08:05 guest Note Added: 0005962
2023-01-13 10:40 guest Note Added: 0005963
2023-01-13 13:11 guest Note Added: 0005964
2023-01-13 14:52 guest Note Added: 0005965
2023-01-13 14:54 guest Note Added: 0005966
2023-01-13 15:29 guest Note Added: 0005967
2023-01-13 16:27 guest Note Added: 0005968
2023-01-13 18:44 guest Note Added: 0005969
2023-04-14 00:50 guest Note Added: 0006318

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