MantisBT - MEGA
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IDProjectCategoryView StatusDate SubmittedLast Update
0001149MEGACalculation Errorpublic2019-03-12 00:392019-03-18 08:35
Reporterguest 
Assigned Togstecher 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusresolvedResolutionno change required 
PlatformPCOSWindowsOS Version7
Product Version 
Target VersionFixed in Version 
First NameQiang
Last NameLi
Email17750225044@163.com
Confirm Email17750225044@163.com
Summary0001149: Inconsistent genetic distance calculation as data increases
DescriptionWith the increase of the number of sequences, the pairwise distances are different. (MEGA 7)
While I was computing the pairwise distances of a FASTA file which including 44 families and 870 sequences, I found if I calculate one family (contains 30 sequences) separately, the pairwise distances of same sequences be different.
For example, the distance between “Cinara pilicornis|ACEA154-14” and “Cinara pilicornis|GBMHH3689-14” is 0.036 in “Aphididae-14.fas” (including 44 families and 870 sequences) and 0.064 in ”Cinara pilicornis.fas” (only one family, 30 sequences).
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Attached Filesrar Upload File.rar (87,639) 2019-03-12 00:39
https://megasoftware.net/mantis_bt/
Issue History
Date ModifiedUsernameFieldChange
2019-03-12 00:39guestNew Issue
2019-03-12 00:39guestFile Added: Upload File.rar
2019-03-18 08:19gstecherNote Deleted: 0001014
2019-03-18 08:19gstecherNote Deleted: 0001023
2019-03-18 08:35gstecherNote Added: 0004208
2019-03-18 08:35gstecherStatusnew => resolved
2019-03-18 08:35gstecherResolutionopen => no change required
2019-03-18 08:35gstecherAssigned To => gstecher

Notes
(0004208)
gstecher   
2019-03-18 08:35   
Hi Qiang,

I am writing in response to your question regarding the MEGA software. The difference in pairwise distances you reported happens because you are using the 'Complete Deletion' option so the data subset used is different between the files. You can use the 'Pairwise Deletion' option if you expect the distances to be the same when using the two input files.