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Unix Source Codes

These programs are used for analysis of Protein and DNA sequences. The programs require a UNIX server to run. See Makefile for how to activate the programs for use. Each program has a different command line for activation. Once the programs are activated, if you are unsure of the commads needed to run a particular program, just type the name of program and press enter. It will describe the process and purpose of the program. If anything, download the Makefile. It has the commands for the programs.

To download these files from a Macintosh, you will have to hold down on the mouse button and drag to "Save As." And right click, if you are on a PC and click "Save As."

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  • Makefile-Makefile from Progressive Alignment of Amino Acid Sequences and Construction of Phylogenetic Trees from Them, by D. F. Feng and R. F. Doolittle, Methods of Enzymology, v266, p368 (1996)
  • Align.c-Program From Progressive Alignment of Amino Acid Sequences and Construction of Phylogenetic Trees from Them, by D. F. Feng and R. F. Doolittle, Methods of Enzymology, v266, p368 (1996)
  • Arrange.c-Program From Progressive Alignment of Amino Acid Sequences and Construction of Phylogenetic Trees from Them, by D. F. Feng and R. F. Doolittle, Methods of Enzymology, v266, p368 (1996)
  • Beta Barrel Finder-The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins econded withing prokaryotic genomes. Zhai, Y., Saier, M.H. Jr., Protein Science. 2002 Sep;11(9):2196-207
  • Blen.c-Program From Progressive Alignment of Amino Acid Sequences and Construction of Phylogenetic Trees from Them, by D. F. Feng and R. F. Doolittle, Methods of Enzymology, v266, p368 (1996)
  • Btree.c-Program From Progressive Alignment of Amino Acid Sequences and Construction of Phylogenetic Trees from Them, by D. F. Feng and R. F. Doolittle, Methods of Enzymology, v266, p368 (1996)
  • Clus.c-Program From Progressive Alignment of Amino Acid Sequences and Construction of Phylogenetic Trees from Them, by D. F. Feng and R. F. Doolittle, Methods of Enzymology, v266, p368 (1996)
  • Crop.c-Program From Progressive Alignment of Amino Acid Sequences and Construction of Phylogenetic Trees from Them, by D. F. Feng and R. F. Doolittle, Methods of Enzymology, v266, p368 (1996)
  • Dayhoff.c-ALIGn program, Dayhoff, M.O., W.C. Barker, and L.T hunt. 1983. Establishing homologies in protein sequences. Methods Enzymol. 91: 524-545.
  • Format.c-Program From Progressive Alignment of Amino Acid Sequences and Construction of Phylogenetic Trees from Them, by D. F. Feng and R. F. Doolittle, Methods of Enzymology, v266, p368 (1996)
  • Inspect.c-Program From Progressive Alignment of Amino Acid Sequences and Construction of Phylogenetic Trees from Them, by D. F. Feng and R. F. Doolittle, Methods of Enzymology, v266, p368 (1996)
  • Mulpub.c-Program From Progressive Alignment of Amino Acid Sequences and Construction of Phylogenetic Trees from Them, by D. F. Feng and R. F. Doolittle, Methods of Enzymology, v266, p368 (1996)
  • Noneg.c-Program From Progressive Alignment of Amino Acid Sequences and Construction of Phylogenetic Trees from Them, by D. F. Feng and R. F. Doolittle, Methods of Enzymology, v266, p368 (1996)
  • Papa3.c-This is the papa3.c program. Reference: R.F. Doolittle & D.F. Feng (1990) Meth. Enzymol., 183:659-669.
  • Prealign.c-Program From Progressive Alignment of Amino Acid Sequences and Construction of Phylogenetic Trees from Them, by D. F. Feng and R. F. Doolittle, Methods of Enzymology, v266, p368 (1996)
  • Setree.c-Program From Progressive Alignment of Amino Acid Sequences and Construction of Phylogenetic Trees from Them, by D. F. Feng and R. F. Doolittle, Methods of Enzymology, v266, p368 (1996)
  • Tree.c-Program From Progressive Alignment of Amino Acid Sequences and Construction of Phylogenetic Trees from Them, by D. F. Feng and R. F. Doolittle, Methods of Enzymology, v266, p368 (1996)
  • Treemoment-Le, T., Tseng, T.-T., and Saier, M.H., Jr. 1999. Flexible programs for the prediction of average amphipathicity of multiply aligned homologous proteins: application to integral membrane transport proteins. Mol. Mem. Biol. 16: 173-179
  • Aachk.c-This program counts the number of residues determined by the user at a given position in an alignment. The percentages are given as averages in a variable window. Developed by Simon Tsang.
  • ChkA.c-This program counts the number of aromatic and aliphatic residues at a given position in an alignment. The percentages are given as averages in a variable window. This program is different than chkALAR2_1 in that data is also gathered for each alignment position. Developed by Simon Tsang.
  • Chkall.c-This program counts the number of strongly polar (D,E,N,Q,K,R,H), anionic (D,E), cationic (R,K,H), semipolar (G,S,T,C), hydroxy (S,T), total hydrophobic (L,I,V,M,F,Y,W,A,P), amphipathic aromatic (Y,W), total aromatic (Y,W,F), total aliphatic (L,I,V,M,A,P), branched chain aliphatic (L,I,V). The percentages are given as averages in a variable window. Developed by Simon Tsang.
  • SuperTree-Ming Ren Yen, Jeehye Choi & Milton H. Saier, Jr. (2009) Bioinformatic Analyses of Transmembrane Transport: Novel Software for Deducing Protein Phylogeny, Topology, and Evolution .
  • GS-Ming Ren Yen, Jeehye Choi & Milton H. Saier, Jr. (2009) Bioinformatic Analyses of Transmembrane Transport: Novel Software for Deducing Protein Phylogeny, Topology, and Evolution
  • makeTable-Ming Ren Yen, Jeehye Choi & Milton H. Saier, Jr. (2009) Bioinformatic Analyses of Transmembrane Transport: Novel Software for Deducing Protein Phylogeny, Topology, and Evolution

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