MantisBT - MEGA
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IDProjectCategoryView StatusDate SubmittedLast Update
0000117MEGADocumentationpublic2016-04-11 06:532016-04-18 08:53
Reporterguest 
Assigned Togstecher 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusresolvedResolutionno change required 
PlatformOSOS Version
Product Version 
Target VersionFixed in Version 
First NameAndreas Sand
Last NamePedersen
EmailAndreas.Pedersen@qiagen.com
Confirm EmailAndreas.Pedersen@qiagen.com
Summary0000117: How does Mega parse newick trees integer IDs on leaves
DescriptionHello,

I am representing QIAGEN Bioinformatics (CLC Genomics Workbench etc.), and I am writing to you because we recently discovered that our importers do not interpret newick trees exported from Mega correctly when it contains nodes with integer IDs.

For example, we will interpret the following tree as having nodes with bootstrap values 1, 2, 3, and 4, while MEGA seems to interpret these values as IDs:

(
  (
    1:1.0,
    2:7.0
  )3:1.0,
  4:3.0
);

We will interpret the same tree as having IDs 1, 2, 3, and 4 if these values are quoted in the newick file.

I am curious how you parse these trees. Do you simply assume that any number attached to an internal node is a bootstrap value, and any number attached to a leaf is an ID? We would consider to do the same if this is what you are doing.

Best regards,
Andreas Sand
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Issue History
Date ModifiedUsernameFieldChange
2016-04-11 06:53guestNew Issue
2016-04-18 08:53gstecherNote Added: 0003648
2016-04-18 08:53gstecherStatusnew => resolved
2016-04-18 08:53gstecherResolutionopen => no change required
2016-04-18 08:53gstecherAssigned To => gstecher

Notes
(0003648)
gstecher   
2016-04-18 08:53   
Hi Andreas,

I am writing in response to your question regarding how MEGA parses newick files. Yes, MEGA assumes that any number attached to an internal node is a bootstrap value (unless it is quoted, in which case it is an ID) and any number attached to a leaf is an ID. But a better way to handle numbers attached to internal nodes would be to ask the user how to interpret the values. This is because bootstrap values are associated with branches but IDs are associated with nodes. In the case where a user re-roots the tree, the interpretation of these values affects how they are displayed. As an example, you can look at how Dendroscope handles the situation.

--
Best regards,

Glen Stecher