[Protdist protein distance matrix] Program=\apps\Protdist.exe Auto-Feed=1 Degap Sequences=0 Auto-Feed File Format=4 Auto-Feed File Name Required=1 Specific File Name=infile Prompt for Input File=0 Prompt for Output File=0 Open Output as Alignment=0 Open Output as Text=0 Open Output with External Program=0 External Program Name= Input File Prefix= Output File Prefix= Specify Input File Name=0 Specify Output File Name=0 Input File Name= Output File Name= Input File Prefix Required=0 Output File Prefix Required=0 Input File Name Arbitrary=0 Output File Name Arbitrary=0 Redirect input from stdin=0 Redirect output from stdout=0 Default Command Line= View Documentation Option=1 Documentation File=\apps\Protdist.doc Description=PROTDIST version 3.5c -- Program to compute distance matrix from protein sequences (c) Copyright 1993 by Joseph Felsenstein. Permission is granted to copy [the documentation] provided that no fee is charged for it and that this copyright notice is not removed. Include Additional Options Box=0 Redirect General stdout=0 Stdout Redirected Filename= Redirect General stdin=1 Stdin Redirected Filename=\apps\phylip.map Additional Output 0 Name=outfile Additional Output 0 Open as Text=1 Additional Output 0 Open as Alignment=0 Additional Output 0 Open with External Program=0 Additional Output 0 External Program Name= Add input file to command line=0 Add output file to command line=0 output command at beginning=0 input command at beginning=0 output command at end=0 input command at end=0 Don't use interface=0 Don't create menu item=0 Remove redundancies=1 Truncate titles=1 Change spaces in titles=1 Open Output with Accessory Application=0 Accessory Application to open with= Space after input prefix=0 Space after output prefix=0 Additional Output 0 Open with Accessory Application=0 Additional Output 0 Accessory Application= Additional Output 0 Rename File=0 Additional Output 0 New File Name= [FastDNAml DNA maximum likelihood] Program=\apps\fastdnaml.EXE Auto-Feed=1 Degap Sequences=0 Auto-Feed File Format=4 Auto-Feed File Name Required=0 Specific File Name= Prompt for Input File=0 Prompt for Output File=0 Open Output as Alignment=0 Open Output as Text=1 Open Output with External Program=0 External Program Name= Input File Prefix= Output File Prefix= Specify Input File Name=1 Specify Output File Name=1 Input File Name= Output File Name= Input File Prefix Required=0 Output File Prefix Required=0 Input File Name Arbitrary=1 Output File Name Arbitrary=1 Redirect input from stdin=1 Redirect output from stdout=1 Default Command Line= View Documentation Option=1 Documentation File=\apps\fastDNAml.doc Description=FastDNAml: A faster derivation of Joe Felsenstein's DNAml, by Gary J. Olsen, Hideo Matsuda, Ray Hagstrom, and Ross Overbeek. Include Additional Options Box=1 Redirect General stdout=0 Stdout Redirected Filename= Redirect General stdin=0 Stdin Redirected Filename= Additional Output 0 Name=treefile.0 Additional Output 0 Open as Text=0 Additional Output 0 Open as Alignment=0 Additional Output 0 Open with External Program=1 Additional Output 0 External Program Name=C:\Program Files\Rod Page\TreeView\treev32.exe Don't use interface=0 Don't create menu item=0 Remove redundancies=0 Truncate titles=0 Change spaces in titles=0 Open Output with Accessory Application=0 Accessory Application to open with= Space after input prefix=0 Space after output prefix=0 Add input file to command line=1 Add output file to command line=1 output command at beginning=0 input command at beginning=0 output command at end=1 input command at end=1 Additional Output 0 Open with Accessory Application=0 Additional Output 0 Accessory Application= Additional Output 0 Rename File=0 Additional Output 0 New File Name= [DNAmlk DNA Maximum Likelihood program with molecular clock] Program=\apps\Dnamlk.exe Auto-Feed=1 Degap Sequences=0 Auto-Feed File Format=4 Auto-Feed File Name Required=1 Specific File Name=infile Prompt for Input File=0 Prompt for Output File=0 Open Output as Alignment=0 Open Output as Text=0 Open Output with External Program=0 External Program Name= Input File Prefix= Output File Prefix= Specify Input File Name=0 Specify Output File Name=0 Input File Name= Output File Name= Input File Prefix Required=0 Output File Prefix Required=0 Input File Name Arbitrary=0 Output File Name Arbitrary=0 Redirect input from stdin=0 Redirect output from stdout=0 Default Command Line= View Documentation Option=1 Documentation File=\apps\Dnamlk.doc Description=DNAMLK version 3.5c -- DNA Maximum Likelihood program with molecular clock (c) Copyright 1986-1993 by Joseph Felsenstein and by the University of Washington. Written by Joseph Felsenstein. Permission is granted to copy [the documentation] provided that no fee is charged for it and that this copyright notice is not removed. Include Additional Options Box=0 Redirect General stdout=0 Stdout Redirected Filename= Redirect General stdin=1 Stdin Redirected Filename=\apps\phylip.map Additional Output 0 Name=outfile Additional Output 0 Open as Text=1 Additional Output 0 Open as Alignment=0 Additional Output 0 Open with External Program=0 Additional Output 0 External Program Name= Additional Output 1 Name=treefile Additional Output 1 Open as Text=1 Additional Output 1 Open as Alignment=0 Additional Output 1 Open with External Program=1 Additional Output 1 External Program Name=C:\Program Files\Rod Page\TreeView\treev32.exe Add input file to command line=0 Add output file to command line=0 output command at beginning=0 input command at beginning=0 output command at end=0 input command at end=0 Don't use interface=0 Don't create menu item=0 Remove redundancies=1 Truncate titles=1 Change spaces in titles=1 Open Output with Accessory Application=0 Accessory Application to open with= Space after input prefix=0 Space after output prefix=0 Additional Output 0 Open with Accessory Application=0 Additional Output 0 Accessory Application= Additional Output 0 Rename File=0 Additional Output 0 New File Name= Additional Output 1 Open with Accessory Application=0 Additional Output 1 Accessory Application= Additional Output 1 Rename File=0 Additional Output 1 New File Name= [DNADist DNA distance matrix] Program=\apps\Dnadist.exe Auto-Feed=1 Degap Sequences=0 Auto-Feed File Format=4 Auto-Feed File Name Required=1 Specific File Name=infile Prompt for Input File=0 Prompt for Output File=0 Open Output as Alignment=0 Open Output as Text=0 Open Output with External Program=0 External Program Name= Input File Prefix= Output File Prefix= Specify Input File Name=0 Specify Output File Name=0 Input File Name= Output File Name= Input File Prefix Required=0 Output File Prefix Required=0 Input File Name Arbitrary=0 Output File Name Arbitrary=0 Redirect input from stdin=0 Redirect output from stdout=0 Default Command Line= View Documentation Option=1 Documentation File=\apps\Dnadist.doc Description=DNADISTversion 3.5c -- Program to compute distance matrix from nucleotide sequences. (c) Copyright 1986-1993 by Joseph Felsenstein and by the University of Washington. Written by Joseph Felsenstein. Permission is granted to copy [the documentation] provided that no fee is charged for it and that this copyright notice is not removed. Include Additional Options Box=0 Redirect General stdout=0 Stdout Redirected Filename= Redirect General stdin=1 Stdin Redirected Filename=\apps\phylip.map Additional Output 0 Name=outfile Additional Output 0 Open as Text=1 Additional Output 0 Open as Alignment=0 Additional Output 0 Open with External Program=0 Additional Output 0 External Program Name= Add input file to command line=0 Add output file to command line=0 output command at beginning=0 input command at beginning=0 output command at end=0 input command at end=0 Don't use interface=0 Don't create menu item=0 Remove redundancies=1 Truncate titles=1 Change spaces in titles=1 Open Output with Accessory Application=0 Accessory Application to open with= Space after input prefix=0 Space after output prefix=0 Additional Output 0 Open with Accessory Application=0 Additional Output 0 Accessory Application= Additional Output 0 Rename File=0 Additional Output 0 New File Name= [Kitsch -- Fitch-Margoliash and Least Squares Methods with Evolutionary Clock] Program=\apps\Kitsch.exe Auto-Feed=0 Degap Sequences=0 Auto-Feed File Format=0 Auto-Feed File Name Required=0 Specific File Name= Prompt for Input File=0 Prompt for Output File=0 Open Output as Alignment=0 Open Output as Text=0 Open Output with External Program=0 External Program Name= Input File Prefix= Output File Prefix= Specify Input File Name=0 Specify Output File Name=0 Input File Name= Output File Name= Input File Prefix Required=0 Output File Prefix Required=0 Input File Name Arbitrary=0 Output File Name Arbitrary=0 Redirect input from stdin=0 Redirect output from stdout=0 Default Command Line= View Documentation Option=1 Documentation File=\apps\Kitsch.doc Description=KITSCH version 3.5c -- Fitch-Margoliash and Least Squares Methods with Evolutionary Clock (c) Copyright 1986-1993 by Joseph Felsenstein and by the University of Washington. Written by Joseph Felsenstein. Permission is granted to copy [the documentation] provided that no fee is charged for it and that this copyright notice is not removed. Include Additional Options Box=0 Redirect General stdout=0 Stdout Redirected Filename= Redirect General stdin=1 Stdin Redirected Filename=\apps\phylip.map Additional Output 0 Name=treefile Additional Output 0 Open as Text=0 Additional Output 0 Open as Alignment=0 Additional Output 0 Open with External Program=1 Additional Output 0 External Program Name=C:\Program Files\Rod Page\TreeView\treev32.exe Additional Output 1 Name=outfile Additional Output 1 Open as Text=1 Additional Output 1 Open as Alignment=0 Additional Output 1 Open with External Program=0 Additional Output 1 External Program Name= Add input file to command line=0 Add output file to command line=0 output command at beginning=0 input command at beginning=0 output command at end=0 input command at end=0 Don't use interface=0 Don't create menu item=0 Remove redundancies=0 Truncate titles=0 Change spaces in titles=0 Open Output with Accessory Application=0 Accessory Application to open with= Space after input prefix=0 Space after output prefix=0 Additional Output 0 Open with Accessory Application=0 Additional Output 0 Accessory Application= Additional Output 0 Rename File=0 Additional Output 0 New File Name= Additional Output 1 Open with Accessory Application=0 Additional Output 1 Accessory Application= Additional Output 1 Rename File=0 Additional Output 1 New File Name= [Fitch -- Fitch-Margoliash and Least-Squares Distance Methods] Program=\apps\Fitch.exe Auto-Feed=0 Degap Sequences=0 Auto-Feed File Format=0 Auto-Feed File Name Required=0 Specific File Name= Prompt for Input File=0 Prompt for Output File=0 Open Output as Alignment=0 Open Output as Text=0 Open Output with External Program=0 External Program Name= Input File Prefix= Output File Prefix= Specify Input File Name=0 Specify Output File Name=0 Input File Name= Output File Name= Input File Prefix Required=0 Output File Prefix Required=0 Input File Name Arbitrary=0 Output File Name Arbitrary=0 Redirect input from stdin=0 Redirect output from stdout=0 Default Command Line= View Documentation Option=1 Documentation File=\apps\Fitch.doc Description=FITCH version 3.5c -- Fitch-Margoliash and Least-Squares Distance Methods. (c) Copyright 1986-1993 by Joseph Felsenstein and by the University of Washington. Written by Joseph Felsenstein. Permission is granted to copy [the documentation] provided that no fee is charged for it and that this copyright notice is not removed. Include Additional Options Box=0 Redirect General stdout=0 Stdout Redirected Filename= Redirect General stdin=1 Stdin Redirected Filename=\apps\phylip.map Additional Output 0 Name=outfile Additional Output 0 Open as Text=1 Additional Output 0 Open as Alignment=0 Additional Output 0 Open with External Program=0 Additional Output 0 External Program Name= Additional Output 1 Name=treefile Additional Output 1 Open as Text=0 Additional Output 1 Open as Alignment=0 Additional Output 1 Open with External Program=1 Additional Output 1 External Program Name=C:\Program Files\Rod Page\TreeView\treev32.exe Add input file to command line=0 Add output file to command line=0 output command at beginning=0 input command at beginning=0 output command at end=0 input command at end=0 Space after input prefix=0 Space after output prefix=0 Don't use interface=0 Don't create menu item=0 Remove redundancies=0 Truncate titles=0 Change spaces in titles=0 Open Output with Accessory Application=0 Accessory Application to open with= Additional Output 0 Open with Accessory Application=0 Additional Output 0 Accessory Application= Additional Output 0 Rename File=0 Additional Output 0 New File Name= Additional Output 1 Open with Accessory Application=0 Additional Output 1 Accessory Application= Additional Output 1 Rename File=0 Additional Output 1 New File Name= [Protpars protein parsimony method] Program=\apps\Protpars.exe Auto-Feed=1 Degap Sequences=0 Auto-Feed File Format=4 Auto-Feed File Name Required=1 Specific File Name=infile Prompt for Input File=0 Prompt for Output File=0 Open Output as Alignment=0 Open Output as Text=0 Open Output with External Program=0 External Program Name= Input File Prefix= Output File Prefix= Specify Input File Name=0 Specify Output File Name=0 Input File Name= Output File Name= Input File Prefix Required=0 Output File Prefix Required=0 Input File Name Arbitrary=0 Output File Name Arbitrary=0 Redirect input from stdin=0 Redirect output from stdout=0 Default Command Line= View Documentation Option=1 Documentation File=\apps\Protpars.doc Description=PROTPARS version 3.5c -- Protein Sequence Parsimony Method. (c) Copyright 1986-1993 by Joseph Felsenstein and by the University of Washington. Written by Joseph Felsenstein. Permission is granted to copy [the documentation] provided that no fee is charged for it and that this copyright notice is not removed. Include Additional Options Box=0 Redirect General stdout=0 Stdout Redirected Filename= Redirect General stdin=1 Stdin Redirected Filename=\apps\phylip.map Additional Output 0 Name=treefile Additional Output 0 Open as Text=0 Additional Output 0 Open as Alignment=0 Additional Output 0 Open with External Program=1 Additional Output 0 External Program Name=C:\Program Files\Rod Page\TreeView\treev32.exe Additional Output 1 Name=outfile Additional Output 1 Open as Text=1 Additional Output 1 Open as Alignment=0 Additional Output 1 Open with External Program=0 Additional Output 1 External Program Name= Add input file to command line=0 Add output file to command line=0 output command at beginning=0 input command at beginning=0 output command at end=0 input command at end=0 Don't use interface=0 Don't create menu item=0 Remove redundancies=1 Truncate titles=1 Change spaces in titles=1 Open Output with Accessory Application=0 Accessory Application to open with= Space after input prefix=0 Space after output prefix=0 Additional Output 0 Open with Accessory Application=0 Additional Output 0 Accessory Application= Additional Output 0 Rename File=0 Additional Output 0 New File Name= Additional Output 1 Open with Accessory Application=0 Additional Output 1 Accessory Application= Additional Output 1 Rename File=0 Additional Output 1 New File Name= [CAP contig assembly program] Program=\apps\cap.EXE Auto-Feed=1 Degap Sequences=1 Auto-Feed File Format=1 Auto-Feed File Name Required=0 Specific File Name= Prompt for Input File=0 Prompt for Output File=0 Open Output as Alignment=1 Open Output as Text=0 Open Output with External Program=0 External Program Name= Input File Prefix= Output File Prefix= Specify Input File Name=1 Specify Output File Name=1 Input File Name= Output File Name= Input File Prefix Required=0 Output File Prefix Required=0 Input File Name Arbitrary=1 Output File Name Arbitrary=1 Redirect input from stdin=0 Redirect output from stdout=0 Default Command Line=>out.sto View Documentation Option=1 Documentation File=\apps\cap.doc Description=CONTIG ASSEMBLY PROGRAM (CAP). copyright (c) 1991. The distribution of the program is granted provided no charge is made and the copyright notice is included. Proper attribution of the author as the source of the software would be appreciated: "A Contig Assembly Program Based on Sensitive Detection of Fragment Overlaps" (submitted to Genomics, 1991). Xiaoqiu Huang. Department of Computer Science. Michigan Technological University. Houghton, MI 49931. E-mail: huang@cs.mtu.edu Include Additional Options Box=1 Redirect General stdout=0 Stdout Redirected Filename= Redirect General stdin=0 Stdin Redirected Filename= i0 Title=Minimum base overlap (no. of bases) i0 Prefix= i0 Default=20 i0 CheckBox=0 i0 CheckBox Title=0 i0 CheckBox Default=0 i1 Title=Percent match (minimum) i1 Prefix= i1 Default=85 i1 CheckBox=0 i1 CheckBox Title=0 i1 CheckBox Default=0 [IdPlot identity plotter] Program=\apps\IdPlot.exe Auto-Feed=1 Degap Sequences=0 Auto-Feed File Format=1 Auto-Feed File Name Required=0 Specific File Name= Prompt for Input File=0 Prompt for Output File=0 Open Output as Alignment=1 Open Output as Text=0 Open Output with External Program=0 External Program Name= Input File Prefix=-i Output File Prefix=-o Specify Input File Name=0 Specify Output File Name=0 Input File Name= Output File Name= Input File Prefix Required=1 Space after input prefix=1 Output File Prefix Required=1 Space after output prefix=1 Input File Name Arbitrary=1 Output File Name Arbitrary=1 Redirect input from stdin=0 Redirect output from stdout=0 Default Command Line= View Documentation Option=0 Documentation File= Description= Include Additional Options Box=0 Redirect General stdout=0 Stdout Redirected Filename= Redirect General stdin=0 Stdin Redirected Filename= Add input file to command line=1 Add output file to command line=1 output command at beginning=1 input command at beginning=1 output command at end=0 input command at end=0 c0 Title=Use consensus sequence as standard (must be named "consensus") c0YES=-c c0NO= c0 Default=0 c1 Title=Verbose c1YES=-v c1NO= c1 Default=0 c2 Title=Ignore gaps in reference sequence c2YES= c2NO=-g c2 Default=1 [NEIGHBOR -- Neighbor-Joining and UPGMA methods] Program=\apps\Neighbor.exe Auto-Feed=0 Degap Sequences=0 Auto-Feed File Format=0 Auto-Feed File Name Required=0 Specific File Name= Prompt for Input File=0 Prompt for Output File=0 Open Output as Alignment=0 Open Output as Text=0 Open Output with External Program=0 External Program Name= Input File Prefix= Output File Prefix= Specify Input File Name=0 Specify Output File Name=0 Input File Name= Output File Name= Input File Prefix Required=0 Space after input prefix=0 Output File Prefix Required=0 Space after output prefix=0 Input File Name Arbitrary=0 Output File Name Arbitrary=0 Redirect input from stdin=0 Redirect output from stdout=0 Default Command Line= View Documentation Option=1 Documentation File=\apps\Neighbor.doc Description=NEIGHBOR -- Neighbor-Joining and UPGMA methods (c) Copyright 1991-1993 by Joseph Felsenstein and by the University of Washington. Written by Joseph Felsenstein. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed Include Additional Options Box=0 Redirect General stdout=0 Stdout Redirected Filename= Redirect General stdin=1 Stdin Redirected Filename=\apps\phylip.map Add input file to command line=0 Add output file to command line=0 output command at beginning=0 input command at beginning=0 output command at end=0 input command at end=0 Additional Output 0 Name=outfile Additional Output 0 Open as Text=1 Additional Output 0 Open as Alignment=0 Additional Output 0 Open with External Program=0 Additional Output 0 External Program Name= Additional Output 1 Name=treefile Additional Output 1 Open as Text=0 Additional Output 1 Open as Alignment=0 Additional Output 1 Open with External Program=1 Additional Output 1 External Program Name=C:\Program Files\Rod Page\TreeView\treev32.exe Don't use interface=0 Don't create menu item=0 Remove redundancies=0 Truncate titles=0 Change spaces in titles=0 Open Output with Accessory Application=0 Accessory Application to open with= Additional Output 0 Open with Accessory Application=0 Additional Output 0 Accessory Application= Additional Output 0 Rename File=0 Additional Output 0 New File Name= Additional Output 1 Open with Accessory Application=0 Additional Output 1 Accessory Application= Additional Output 1 Rename File=0 Additional Output 1 New File Name= [DNADist ---> Neighbor phylogenetic tree] Program=\apps\Dnadist.exe Don't use interface=0 Don't create menu item=0 Auto-Feed=1 Degap Sequences=0 Auto-Feed File Format=4 Auto-Feed File Name Required=1 Remove redundancies=0 Truncate titles=0 Change spaces in titles=0 Specific File Name=infile Prompt for Input File=0 Prompt for Output File=0 Open Output as Alignment=0 Open Output as Text=0 Open Output with External Program=0 External Program Name= Open Output with Accessory Application=0 Accessory Application to open with= Input File Prefix= Output File Prefix= Specify Input File Name=0 Specify Output File Name=0 Input File Name= Output File Name= Input File Prefix Required=0 Space after input prefix=0 Output File Prefix Required=0 Space after output prefix=0 Input File Name Arbitrary=0 Output File Name Arbitrary=0 Redirect input from stdin=0 Redirect output from stdout=0 Default Command Line= View Documentation Option=1 Documentation File=\apps\Dnadist.doc Description=DNADISTversion 3.5c -- Program to compute distance matrix from nucleotide sequences. (c) Copyright 1986-1993 by Joseph Felsenstein and by the University of Washington. Written by Joseph Felsenstein. Permission is granted to copy [the documentation] provided that no fee is charged for it and that this copyright notice is not removed. Include Additional Options Box=0 Redirect General stdout=0 Stdout Redirected Filename= Redirect General stdin=1 Stdin Redirected Filename=\apps\phylip.map Add input file to command line=0 Add output file to command line=0 output command at beginning=0 input command at beginning=0 output command at end=0 input command at end=0 Additional Output 0 Name=outfile Additional Output 0 Open as Text=1 Additional Output 0 Open as Alignment=0 Additional Output 0 Open with External Program=0 Additional Output 0 External Program Name= Additional Output 0 Open with Accessory Application=1 Additional Output 0 Accessory Application=Neighbor link for DNADist -> Neighbor Additional Output 0 Rename File=1 Additional Output 0 New File Name=infile [Neighbor link for DNADist -> Neighbor] Program=\apps\Neighbor.exe Don't use interface=1 Don't create menu item=1 Auto-Feed=0 Degap Sequences=0 Auto-Feed File Format=0 Auto-Feed File Name Required=0 Remove redundancies=0 Truncate titles=0 Change spaces in titles=0 Specific File Name= Prompt for Input File=0 Prompt for Output File=0 Open Output as Alignment=0 Open Output as Text=0 Open Output with External Program=0 External Program Name= Open Output with Accessory Application=0 Accessory Application to open with= Input File Prefix= Output File Prefix= Specify Input File Name=0 Specify Output File Name=0 Input File Name= Output File Name= Input File Prefix Required=0 Space after input prefix=0 Output File Prefix Required=0 Space after output prefix=0 Input File Name Arbitrary=0 Output File Name Arbitrary=0 Redirect input from stdin=0 Redirect output from stdout=0 Default Command Line= View Documentation Option=1 Documentation File=\apps\Neighbor.doc Description=NEIGHBOR -- Neighbor-Joining and UPGMA methods (c) Copyright 1991-1993 by Joseph Felsenstein and by the University of Washington. Written by Joseph Felsenstein. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed Include Additional Options Box=0 Redirect General stdout=0 Stdout Redirected Filename= Redirect General stdin=1 Stdin Redirected Filename=\apps\phylip.map Add input file to command line=0 Add output file to command line=0 output command at beginning=0 input command at beginning=0 output command at end=0 input command at end=0 Additional Output 0 Name=outfile Additional Output 0 Open as Text=1 Additional Output 0 Open as Alignment=0 Additional Output 0 Open with External Program=0 Additional Output 0 External Program Name= Additional Output 0 Open with Accessory Application=0 Additional Output 0 Accessory Application= Additional Output 0 Rename File=0 Additional Output 0 New File Name= Additional Output 1 Name=treefile Additional Output 1 Open as Text=0 Additional Output 1 Open as Alignment=0 Additional Output 1 Open with External Program=1 Additional Output 1 External Program Name=C:\Program Files\Rod Page\TreeView\treev32.exe Additional Output 1 Open with Accessory Application=0 Additional Output 1 Accessory Application= Additional Output 1 Rename File=0 Additional Output 1 New File Name= [Protdist ---> Fitch phylogenetic tree] Program=\apps\Protdist.exe Don't use interface=0 Don't create menu item=0 Auto-Feed=1 Degap Sequences=0 Auto-Feed File Format=4 Auto-Feed File Name Required=1 Remove redundancies=1 Truncate titles=1 Change spaces in titles=1 Specific File Name=infile Prompt for Input File=0 Prompt for Output File=0 Open Output as Alignment=0 Open Output as Text=0 Open Output with External Program=0 External Program Name= Open Output with Accessory Application=0 Accessory Application to open with= Input File Prefix= Output File Prefix= Specify Input File Name=0 Specify Output File Name=0 Input File Name= Output File Name= Input File Prefix Required=0 Space after input prefix=0 Output File Prefix Required=0 Space after output prefix=0 Input File Name Arbitrary=0 Output File Name Arbitrary=0 Redirect input from stdin=0 Redirect output from stdout=0 Default Command Line= View Documentation Option=1 Documentation File=\apps\Protdist.doc Description=PROTDIST version 3.5c -- Program to compute distance matrix from protein sequences (c) Copyright 1993 by Joseph Felsenstein. Permission is granted to copy [the documentation] provided that no fee is charged for it and that this copyright notice is not removed. Include Additional Options Box=0 Redirect General stdout=0 Stdout Redirected Filename= Redirect General stdin=1 Stdin Redirected Filename=\apps\phylip.map Add input file to command line=0 Add output file to command line=0 output command at beginning=0 input command at beginning=0 output command at end=0 input command at end=0 Additional Output 0 Name=outfile Additional Output 0 Open as Text=1 Additional Output 0 Open as Alignment=0 Additional Output 0 Open with External Program=0 Additional Output 0 External Program Name= Additional Output 0 Open with Accessory Application=1 Additional Output 0 Accessory Application=Fitch link for Protdist -> Fitch tree Additional Output 0 Rename File=1 Additional Output 0 New File Name=infile [Fitch link for Protdist -> Fitch tree] Program=\apps\Fitch.exe Don't use interface=1 Don't create menu item=1 Auto-Feed=0 Degap Sequences=0 Auto-Feed File Format=0 Auto-Feed File Name Required=0 Remove redundancies=0 Truncate titles=0 Change spaces in titles=0 Specific File Name= Prompt for Input File=0 Prompt for Output File=0 Open Output as Alignment=0 Open Output as Text=0 Open Output with External Program=0 External Program Name= Open Output with Accessory Application=0 Accessory Application to open with= Input File Prefix= Output File Prefix= Specify Input File Name=0 Specify Output File Name=0 Input File Name= Output File Name= Input File Prefix Required=0 Space after input prefix=0 Output File Prefix Required=0 Space after output prefix=0 Input File Name Arbitrary=0 Output File Name Arbitrary=0 Redirect input from stdin=0 Redirect output from stdout=0 Default Command Line= View Documentation Option=1 Documentation File=\apps\Fitch.doc Description=FITCH version 3.5c -- Fitch-Margoliash and Least-Squares Distance Methods. (c) Copyright 1986-1993 by Joseph Felsenstein and by the University of Washington. Written by Joseph Felsenstein. Permission is granted to copy [the documentation] provided that no fee is charged for it and that this copyright notice is not removed. Include Additional Options Box=0 Redirect General stdout=0 Stdout Redirected Filename= Redirect General stdin=1 Stdin Redirected Filename=\apps\phylip.map Add input file to command line=0 Add output file to command line=0 output command at beginning=0 input command at beginning=0 output command at end=0 input command at end=0 Additional Output 0 Name=outfile Additional Output 0 Open as Text=1 Additional Output 0 Open as Alignment=0 Additional Output 0 Open with External Program=0 Additional Output 0 External Program Name= Additional Output 0 Open with Accessory Application=0 Additional Output 0 Accessory Application= Additional Output 0 Rename File=0 Additional Output 0 New File Name= Additional Output 1 Name=treefile Additional Output 1 Open as Text=0 Additional Output 1 Open as Alignment=0 Additional Output 1 Open with External Program=1 Additional Output 1 External Program Name=C:\Program Files\Rod Page\TreeView\treev32.exe Additional Output 1 Open with Accessory Application=0 Additional Output 1 Accessory Application= Additional Output 1 Rename File=0 Additional Output 1 New File Name=