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Re: Editing character matrices

----- Original Message -----
From: "Mike Taylor" <mike@indexdata.com>
Sent: Friday, May 18, 2007 12:07 AM

What do you all use for editing your character matrices?  Up till now,
I've been editing the Nexus file by hand using a text-editor.  That
was OK when I was just adding taxa, but is going to be way cumbersome
now I'm adding characters, too.  Thanks for all suggestions, other
than Mesquite.  (Please, no-one recommend that!)

What's bad about Mesquite? If it keeps crashing, make sure you've installed the latest versions of both Mesquite and Java (Java Virtual Machine in Windows). Sure, it bloats every file it touches, but it doesn't make them unrecognisable.

That said, I've never used it as a data matrix editor. I've used the NDE, the Nexus Data Editor by Rod Page. Just google for it. It's good, and free, but it has one problem: it doesn't understand the full range of possibilities a Nexus file supports, so it deletes certain things it doesn't understand from Nexus files you save in it, and I have a Nexus file that runs fine in PAUP* but that the NDE refuses to open. (Maybe there's a newer version of the NDE by now, however. I haven't checked in years.)

This file I treated with PAUP* itself. PAUP* is a decent text editor, especially in Windows where it supports the Alt + drag trick that lets you highlight columns of text rather than just lines. You just have to (manually) put enough whitespace into the matrix so you don't lose track... and if you open the file in the NDE after that, the NDE will annoyingly rearrange it, putting a space behind every 10 characters and deleting whitespace elsewhere.

On a Mac I of course recommend MacClade. I've used it, though on a rather simple file, so I don't know if it shares the quirks of the NDE.