0000117: How does Mega parse newick trees integer IDs on leaves

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0000117

MEGA

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public

2016-04-11 06:53

2016-04-18 08:53

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guest

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gstecher

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normal

Severity

minor

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have not tried

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resolved

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no change required

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Summary

0000117: How does Mega parse newick trees integer IDs on leaves

Description

Hello,

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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Andreas Sand

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Pedersen

Andreas.Pedersen@qiagen.com

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Andreas.Pedersen@qiagen.com

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Notes
(0003648) gstecher (administrator) 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

Issue History
Date Modified	Username	Field	Change
2016-04-11 06:53	guest	New Issue
2016-04-18 08:53	gstecher	Note Added: 0003648
2016-04-18 08:53	gstecher	Status	new => resolved
2016-04-18 08:53	gstecher	Resolution	open => no change required
2016-04-18 08:53	gstecher	Assigned To	=> gstecher