Suggestions for PHYLIP

Doug_Eernisse at UB.CC.UMICH.EDU Doug_Eernisse at UB.CC.UMICH.EDU
Mon Nov 26 10:25:56 EST 1990

PAUP 3.0 was officially released by the Hennig meetings in Fall of 1989 but
I received a slightly updated 3.0a version from the author, David Swofford,
on 12/13/89. I heard from him recently and he is up to at least 3.0m, but
he may be waiting for his upcoming 3.1 release which will have the real
(not draft) version of the manual before he responds to requests.
I have recently released a HyperCard 2.0 stack which does a good job of
converting from various formats of aligned sequence data, or data from
GenBank, EMBL, other programs, etc. for singles sequences, to the format
required by PAUP 3.0/ MacClade (unreleased 3.0 version), PHYLIP 3.3, 
and Hennig86, or between these formats. The stack also does other things.
Here is a short blurb about it:
                       About DNA Translator stack 
                     Version .96  November 21, 1990 
                        Copyright 1990  D. J. Eernisse
The DNA Translator HyperCard stack facilitates three different but 
complementary functions. First, DNA Translator displays codon and 
amino acid usage data as it differs for different organelles and 
organisms, with emphasis on animal mitochondrial DNA (mtDNA). The 
first function uses 64 "codon" cards, featuring graphical displays 
of codon usage as it varies for different organisms. Second, a "gene 
mapping" card displays two linear gene maps which are automatically 
drawn at desired scales and locations ranging from 10 to 100 percent 
of the total gene length, with data provided for the nine animal 
taxa for which complete mtDNA sequences are available. Gene 
sequences for these taxa may be extracted by clicking on a displayed 
gene. Third, the stack features file conversion functions on 
"utility" cards, mostly for converting aligned sequence data to an 
appropriate format for phylogenetic analysis using parsimony 
methods, or vice versa, but also some general utilities for 
manipulation of sequence data, including translation of nucleotides 
to peptides, sequence entry, and various format conversions. The 
codon usage, gene map and utility functions are essentially 
independent functions, although sequences extracted from the gene 
mapping card may be used on utility cards.
This version of the stack requires HyperCard 2.0, which also means 
that you need Macintosh System 6.0.5 or greater. For optimal 
performance, you will probably need to install it to a hard disk on 
a Macintosh with a minimum of 2 MB RAM. 
I would be grateful for comments and suggestions or sample aligned 
data files from a program that you might use. Please let me know if 
the exported files may encounter problems when used by other 
programs. I may be contacted at:
Email Internet:    usergdef at ub.cc.umich.edu 
Email Bitnet:      usergdef at umichub
Office Phone:      (313) 747-2193
Mailing Address:   Museum of Zoology
                   University of Michigan
                   Ann Arbor, MI 48109-1079 USA
If you use this software for studies that result in publication, 
please cite as:
Eernisse, D. J. 1990. DNA Translator, a HyperCard* stack for 
molecular systematics.  Published electronically on the Internet, 
available via anonymous ftp to iubio.bio.indiana.edu.
Permission is hereby granted to distribute the complete and
unmodified version of the HyperCard stack, DNA Translator, provided 
that distribution is for nonprofit purposes only. Although this 
stack is freeware, it is not public domain. I (D. J. Eernisse) 
retain all rights of distribution. The stack also uses several XCMDs 
and XFCNs that are available for noncommercial use but have similar 
copyright restrictions (see stack script for credits). 
If you want a copy of this stack, and are unable to download it from 
IuBio.Bio.Indiana.Edu (submitted there 11/21/90,then send a S.A.S.E. 
and a blank disk, or $6 if you want me to provide the postage and 
disk, to: D. J. Eernisse, Museum of Zoology, University of Michigan, 
Ann Arbor, MI 48109-1079. 
Alternatively, the most current version of the stack will be kept 
available, at least temporarily, by anonymous ftp to 
ub.cc.umich.edu. If you have access to the Internet through a 
University mainframe system, chances are you are able to ftp. Type 
'$ftp ub.cc.umich.edu' from your Internet host, login as 
'anonymous', type 'guest' for password, then type 'get gdef/DNAstack 
yourflnm' where 'yourflnm' is an optional filename of your choice. 
You will need to debinhex it with the widely available freeware 
BinHex 4.0 or the shareware compaction archive utility StuffIt 1.5.1 
(or the freeware UnStuffIt). You then can decompress the stack by 
double-clicking on the Compactor self extracting archive 
(DNAstack.sea) from the Finder.
That is the end of the blurb. Unfortunately, the stack no longer runs
on earlier versions of HyperCard, so you will have to visit an Apple
dealer or your campus software distributor for a "free" upgrade.
There are also facilities to go back and forth between an interleaved
with or without match characters and straight string sequences.

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