fprotpars Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Protein parsimony algorithm Description Estimates phylogenies from protein sequences (input using the standard one-letter code for amino acids) using the parsimony method, in a variant which counts only those nucleotide changes that change the amino acid, on the assumption that silent changes are more easily accomplished. Algorithm This program infers an unrooted phylogeny from protein sequences, using a new method intermediate between the approaches of Eck and Dayhoff (1966) and Fitch (1971). Eck and Dayhoff (1966) allowed any amino acid to change to any other, and counted the number of such changes needed to evolve the protein sequences on each given phylogeny. This has the problem that it allows replacements which are not consistent with the genetic code, counting them equally with replacements that are consistent. Fitch, on the other hand, counted the minimum number of nucleotide substitutions that would be needed to achieve the given protein sequences. This counts silent changes equally with those that change the amino acid. The present method insists that any changes of amino acid be consistent with the genetic code so that, for example, lysine is allowed to change to methionine but not to proline. However, changes between two amino acids via a third are allowed and counted as two changes if each of the two replacements is individually allowed. This sometimes allows changes that at first sight you would think should be outlawed. Thus we can change from phenylalanine to glutamine via leucine in two steps total. Consulting the genetic code, you will find that there is a leucine codon one step away from a phenylalanine codon, and a leucine codon one step away from glutamine. But they are not the same leucine codon. It actually takes three base substitutions to get from either of the phenylalanine codons TTT and TTC to either of the glutamine codons CAA or CAG. Why then does this program count only two? The answer is that recent DNA sequence comparisons seem to show that synonymous changes are considerably faster and easier than ones that change the amino acid. We are assuming that, in effect, synonymous changes occur so much more readily that they need not be counted. Thus, in the chain of changes TTT (Phe) --> CTT (Leu) --> CTA (Leu) --> CAA (Glu), the middle one is not counted because it does not change the amino acid (leucine). To maintain consistency with the genetic code, it is necessary for the program internally to treat serine as two separate states (ser1 and ser2) since the two groups of serine codons are not adjacent in the code. Changes to the state "deletion" are counted as three steps to prevent the algorithm from assuming unnecessary deletions. The state "unknown" is simply taken to mean that the amino acid, which has not been determined, will in each part of a tree that is evaluated be assumed be whichever one causes the fewest steps. The assumptions of this method (which has not been described in the literature), are thus something like this: Change in different sites is independent. Change in different lineages is independent. The probability of a base substitution that changes the amino acid sequence is small over the lengths of time involved in a branch of the phylogeny. The expected amounts of change in different branches of the phylogeny do not vary by so much that two changes in a high-rate branch are more probable than one change in a low-rate branch. The expected amounts of change do not vary enough among sites that two changes in one site are more probable than one change in another. The probability of a base change that is synonymous is much higher than the probability of a change that is not synonymous. That these are the assumptions of parsimony methods has been documented in a series of papers of mine: (1973a, 1978b, 1979, 1981b, 1983b, 1988b). For an opposing view arguing that the parsimony methods make no substantive assumptions such as these, see the works by Farris (1983) and Sober (1983a, 1983b, 1988), but also read the exchange between Felsenstein and Sober (1986). The input for the program is fairly standard. The first line contains the number of species and the number of amino acid positions (counting any stop codons that you want to include). Next come the species data. Each sequence starts on a new line, has a ten-character species name that must be blank-filled to be of that length, followed immediately by the species data in the one-letter code. The sequences must either be in the "interleaved" or "sequential" formats described in the Molecular Sequence Programs document. The I option selects between them. The sequences can have internal blanks in the sequence but there must be no extra blanks at the end of the terminated line. Note that a blank is not a valid symbol for a deletion. The protein sequences are given by the one-letter code used by described in the Molecular Sequence Programs documentation file. Note that if two polypeptide chains are being used that are of different length owing to one terminating before the other, they should be coded as (say) HIINMA*???? HIPNMGVWABT since after the stop codon we do not definitely know that there has been a deletion, and do not know what amino acid would have been there. If DNA studies tell us that there is DNA sequence in that region, then we could use "X" rather than "?". Note that "X" means an unknown amino acid, but definitely an amino acid, while "?" could mean either that or a deletion. The distinction is often significant in regions where there are deletions: one may want to encode a six-base deletion as "-?????" since that way the program will only count one deletion, not six deletion events, when the deletion arises. However, if there are overlapping deletions it may not be so easy to know what coding is correct. One will usually want to use "?" after a stop codon, if one does not know what amino acid is there. If the DNA sequence has been observed there, one probably ought to resist putting in the amino acids that this DNA would code for, and one should use "X" instead, because under the assumptions implicit in this parsimony method, changes to any noncoding sequence are much easier than changes in a coding region that change the amino acid, so that they shouldn't be counted anyway! The form of this information is the standard one described in the main documentation file. For the U option the tree provided must be a rooted bifurcating tree, with the root placed anywhere you want, since that root placement does not affect anything. Usage Here is a sample session with fprotpars % fprotpars Protein parsimony algorithm Input (aligned) protein sequence set(s): protpars.dat Phylip tree file (optional): Phylip protpars program output file [protpars.fprotpars]: Adding species: 1. Alpha 2. Beta 3. Gamma 4. Delta 5. Epsilon Doing global rearrangements !---------! ......... ......... Output written to file "protpars.fprotpars" Trees also written onto file "protpars.treefile" Done. Go to the input files for this example Go to the output files for this example Example 2 % fprotpars -njumble 3 -seed 3 -printdata -ancseq -whichcode m -stepbox -outgrno 2 -dothreshold -threshold 3 Protein parsimony algorithm Input (aligned) protein sequence set(s): protpars.dat Phylip tree file (optional): Phylip protpars program output file [protpars.fprotpars]: Adding species: 1. Delta 2. Epsilon 3. Alpha 4. Beta 5. Gamma Doing global rearrangements !---------! ......... ......... Adding species: 1. Beta 2. Epsilon 3. Delta 4. Alpha 5. Gamma Doing global rearrangements !---------! ......... Adding species: 1. Epsilon 2. Alpha 3. Gamma 4. Delta 5. Beta Doing global rearrangements !---------! ......... Output written to file "protpars.fprotpars" Trees also written onto file "protpars.treefile" Done. Go to the output files for this example Example 3 % fprotpars -njumble 3 -seed 3 Protein parsimony algorithm Input (aligned) protein sequence set(s): protpars2.dat Phylip tree file (optional): Phylip protpars program output file [protpars2.fprotpars]: Data set # 1: Adding species: 1. Delta 2. Epsilon 3. Alpha 4. Beta 5. Gamma Doing global rearrangements !---------! ......... ......... Adding species: 1. Beta 2. Epsilon 3. Delta 4. Alpha 5. Gamma Doing global rearrangements !---------! ......... Adding species: 1. Epsilon 2. Alpha 3. Gamma 4. Delta 5. Beta Doing global rearrangements !---------! ......... Output written to file "protpars2.fprotpars" Trees also written onto file "protpars2.treefile" Data set # 2: Adding species: 1. Gamma 2. Delta 3. Epsilon 4. Beta 5. Alpha Doing global rearrangements !---------! ......... ......... Adding species: 1. Alpha 2. Delta 3. Epsilon 4. Gamma 5. Beta Doing global rearrangements !---------! ......... Adding species: 1. Epsilon 2. Beta 3. Gamma 4. Alpha 5. Delta Doing global rearrangements !---------! ......... Output written to file "protpars2.fprotpars" Trees also written onto file "protpars2.treefile" Data set # 3: Adding species: 1. Delta 2. Beta 3. Gamma 4. Alpha 5. Epsilon Doing global rearrangements !---------! ......... ......... Adding species: 1. Gamma 2. Delta 3. Beta 4. Epsilon 5. Alpha Doing global rearrangements !---------! ......... Adding species: 1. Epsilon 2. Alpha 3. Gamma 4. Delta 5. Beta Doing global rearrangements !---------! ......... Output written to file "protpars2.fprotpars" Trees also written onto file "protpars2.treefile" Done. Go to the input files for this example Go to the output files for this example Example 4 % fprotpars -option Protein parsimony algorithm Input (aligned) protein sequence set(s): protpars.dat Phylip tree file (optional): Phylip weights file (optional): protparswts.dat Number of times to randomise [0]: Species number to use as outgroup [0]: Use threshold parsimony [N]: Genetic codes U : Universal M : Mitochondrial V : Vertebrate mitochondrial F : Fly mitochondrial Y : Yeast mitochondrial Use which genetic code [Universal]: Phylip protpars program output file [protpars.fprotpars]: Write out trees to tree file [Y]: Phylip tree output file (optional) [protpars.treefile]: Print data at start of run [N]: Print indications of progress of run [Y]: Print out tree [Y]: Print steps at each site [N]: Print sequences at all nodes of tree [N]: Weights set # 1: Adding species: 1. Delta 2. Alpha 3. Gamma 4. Epsilon 5. Beta Doing global rearrangements !---------! ......... ......... Output written to file "protpars.fprotpars" Trees also written onto file "protpars.treefile" Weights set # 2: Adding species: 1. Epsilon 2. Alpha 3. Delta 4. Gamma 5. Beta Doing global rearrangements !---------! ......... ......... Output written to file "protpars.fprotpars" Trees also written onto file "protpars.treefile" Done. Go to the input files for this example Go to the output files for this example Command line arguments Protein parsimony algorithm Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-sequence] seqsetall File containing one or more sequence alignments [-intreefile] tree Phylip tree file (optional) [-outfile] outfile [*.fprotpars] Phylip protpars program output file Additional (Optional) qualifiers (* if not always prompted): -weights properties Phylip weights file (optional) * -njumble integer [0] Number of times to randomise (Integer 0 or more) * -seed integer [1] Random number seed between 1 and 32767 (must be odd) (Integer from 1 to 32767) -outgrno integer [0] Species number to use as outgroup (Integer 0 or more) -dothreshold toggle [N] Use threshold parsimony * -threshold float [1] Threshold value (Number 1.000 or more) -whichcode menu [Universal] Use which genetic code (Values: U (Universal); M (Mitochondrial); V (Vertebrate mitochondrial); F (Fly mitochondrial); Y (Yeast mitochondrial)) -[no]trout toggle [Y] Write out trees to tree file * -outtreefile outfile [*.fprotpars] Phylip tree output file (optional) -printdata boolean [N] Print data at start of run -[no]progress boolean [Y] Print indications of progress of run -[no]treeprint boolean [Y] Print out tree -stepbox boolean [N] Print steps at each site -ancseq boolean [N] Print sequences at all nodes of tree * -[no]dotdiff boolean [Y] Use dot differencing to display results Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -scircular1 boolean Sequence is circular -squick1 boolean Read id and sequence only -sformat1 string Input sequence format -iquery1 string Input query fields or ID list -ioffset1 integer Input start position offset -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-outfile" associated qualifiers -odirectory3 string Output directory "-outtreefile" associated qualifiers -odirectory string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit Input file format fprotpars reads any normal sequence USAs. Input files for usage example File: protpars.dat 5 10 Alpha ABCDEFGHIK Beta AB--EFGHIK Gamma ?BCDSFG*?? Delta CIKDEFGHIK Epsilon DIKDEFGHIK Input files for usage example 3 File: protpars2.dat 5 10 Alpha AABBCCCFHK Beta AABB---FHK Gamma ??BBCCCF*? Delta CCIIKKKFHK Epsilon DDIIKKKFHK 5 10 Alpha AADDEGGIIK Beta AA--EGGIIK Gamma ??DDSGG??? Delta CCDDEGGIIK Epsilon DDDDEGGIIK 5 10 Alpha AACDDDEGHI Beta AA----EGHI Gamma ??CDDDSG*? Delta CCKDDDEGHI Epsilon DDKDDDEGHI Input files for usage example 4 File: protparswts.dat 1111100000 0000011111 Output file format fprotpars output is standard: if option 1 is toggled on, the data is printed out, with the convention that "." means "the same as in the first species". Then comes a list of equally parsimonious trees, and (if option 2 is toggled on) a table of the number of changes of state required in each position. If option 5 is toggled on, a table is printed out after each tree, showing for each branch whether there are known to be changes in the branch, and what the states are inferred to have been at the top end of the branch. This is a reconstruction of the ancestral sequences in the tree. If you choose option 5, a menu item "." appears which gives you the opportunity to turn off dot-differencing so that complete ancestral sequences are shown. If the inferred state is a "?" there will be multiple equally-parsimonious assignments of states; the user must work these out for themselves by hand. If option 6 is left in its default state the trees found will be written to a tree file, so that they are available to be used in other programs. If the program finds multiple trees tied for best, all of these are written out onto the output tree file. Each is followed by a numerical weight in square brackets (such as [0.25000]). This is needed when we use the trees to make a consensus tree of the results of bootstrapping or jackknifing, to avoid overrepresenting replicates that find many tied trees. If the U (User Tree) option is used and more than one tree is supplied, the program also performs a statistical test of each of these trees against the best tree. This test, which is a version of the test proposed by Alan Templeton (1983) and evaluated in a test case by me (1985a). It is closely parallel to a test using log likelihood differences due to Kishino and Hasegawa (1989), and uses the mean and variance of step differences between trees, taken across positions. If the mean is more than 1.96 standard deviations different then the trees are declared significantly different. The program prints out a table of the steps for each tree, the differences of each from the best one, the variance of that quantity as determined by the step differences at individual positions, and a conclusion as to whether that tree is or is not significantly worse than the best one. Output files for usage example File: protpars.fprotpars Protein parsimony algorithm, version 3.69.650 3 trees in all found +--------Gamma ! +--2 +--Epsilon ! ! +--4 ! +--3 +--Delta 1 ! ! +-----Beta ! +-----------Alpha remember: this is an unrooted tree! requires a total of 16.000 +--Epsilon +--4 +--3 +--Delta ! ! +--2 +-----Gamma ! ! 1 +--------Beta ! +-----------Alpha remember: this is an unrooted tree! requires a total of 16.000 +--Epsilon +-----4 ! +--Delta +--3 ! ! +--Gamma 1 +-----2 ! +--Beta ! +-----------Alpha remember: this is an unrooted tree! requires a total of 16.000 File: protpars.treefile ((Gamma,((Epsilon,Delta),Beta)),Alpha)[0.3333]; ((((Epsilon,Delta),Gamma),Beta),Alpha)[0.3333]; (((Epsilon,Delta),(Gamma,Beta)),Alpha)[0.3333]; Output files for usage example 2 File: protpars.fprotpars Protein parsimony algorithm, version 3.69.650 5 species, 10 sites Name Sequences ---- --------- Alpha ABCDEFGHIK Beta ..--...... Gamma ?...S..*?? Delta CIK....... Epsilon DIK....... 3 trees in all found +-----------Beta ! 1 +--------Gamma ! ! +--2 +--Epsilon ! +--4 +--3 +--Delta ! +-----Alpha remember: (although rooted by outgroup) this is an unrooted tree! requires a total of 14.000 steps in each position: 0 1 2 3 4 5 6 7 8 9 *----------------------------------------- 0! 3 1 5 3 2 0 0 2 0 10! 0 From To Any Steps? State at upper node ( . means same as in the node below it on tree) root 1 AN??EFGHIK 1 Beta maybe .B--...... [Part of this file has been deleted for brevity] root 1 AN??EFGHIK 1 Beta maybe .B--...... 1 2 maybe ..CD...... 2 3 maybe ?......... 3 4 yes .IK....... 4 Epsilon maybe D......... 4 Delta yes C......... 3 Gamma yes ?B..S..*?? 2 Alpha maybe .B........ +-----------Beta ! 1 +--Epsilon ! +-----4 ! ! +--Delta +--3 ! +--Gamma +-----2 +--Alpha remember: (although rooted by outgroup) this is an unrooted tree! requires a total of 14.000 steps in each position: 0 1 2 3 4 5 6 7 8 9 *----------------------------------------- 0! 3 1 5 3 2 0 0 2 0 10! 0 From To Any Steps? State at upper node ( . means same as in the node below it on tree) root 1 AN??EFGHIK 1 Beta maybe .B--...... 1 3 yes ..?D...... 3 4 yes ?IK....... 4 Epsilon maybe D......... 4 Delta yes C......... 3 2 yes ..C....... 2 Gamma yes ?B..S..*?? 2 Alpha maybe .B........ File: protpars.treefile (Beta,(Gamma,((Epsilon,Delta),Alpha)))[0.3333]; (Beta,(((Epsilon,Delta),Gamma),Alpha))[0.3333]; (Beta,((Epsilon,Delta),(Gamma,Alpha)))[0.3333]; Output files for usage example 3 File: protpars2.fprotpars Protein parsimony algorithm, version 3.69.650 Data set # 1: 3 trees in all found +--------Gamma ! +--2 +--Epsilon ! ! +--4 ! +--3 +--Delta 1 ! ! +-----Beta ! +-----------Alpha remember: this is an unrooted tree! requires a total of 25.000 +--Epsilon +--4 +--3 +--Delta ! ! +--2 +-----Gamma ! ! 1 +--------Beta ! +-----------Alpha remember: this is an unrooted tree! requires a total of 25.000 +--Epsilon +-----4 [Part of this file has been deleted for brevity] +--------Gamma +--2 ! ! +-----Epsilon ! +--4 1 ! +--Delta ! +--3 ! +--Beta ! +-----------Alpha remember: this is an unrooted tree! requires a total of 24.000 +--Epsilon +--4 +--3 +--Delta ! ! +--2 +-----Gamma ! ! 1 +--------Beta ! +-----------Alpha remember: this is an unrooted tree! requires a total of 24.000 +--Epsilon +-----4 ! +--Delta +--3 ! ! +--Gamma 1 +-----2 ! +--Beta ! +-----------Alpha remember: this is an unrooted tree! requires a total of 24.000 File: protpars2.treefile ((Gamma,((Epsilon,Delta),Beta)),Alpha)[0.3333]; ((((Epsilon,Delta),Gamma),Beta),Alpha)[0.3333]; (((Epsilon,Delta),(Gamma,Beta)),Alpha)[0.3333]; ((Gamma,(Delta,(Epsilon,Beta))),Alpha)[0.0667]; (((Epsilon,Gamma),(Delta,Beta)),Alpha)[0.0667]; ((Gamma,((Epsilon,Delta),Beta)),Alpha)[0.0667]; ((Epsilon,(Gamma,(Delta,Beta))),Alpha)[0.0667]; ((Gamma,(Epsilon,(Delta,Beta))),Alpha)[0.0667]; (((Delta,Gamma),(Epsilon,Beta)),Alpha)[0.0667]; (((Delta,(Epsilon,Gamma)),Beta),Alpha)[0.0667]; ((((Epsilon,Delta),Gamma),Beta),Alpha)[0.0667]; ((Epsilon,((Delta,Gamma),Beta)),Alpha)[0.0667]; (((Epsilon,(Delta,Gamma)),Beta),Alpha)[0.0667]; ((Delta,(Gamma,(Epsilon,Beta))),Alpha)[0.0667]; ((Delta,((Epsilon,Gamma),Beta)),Alpha)[0.0667]; (((Epsilon,Delta),(Gamma,Beta)),Alpha)[0.0667]; ((Delta,(Epsilon,(Gamma,Beta))),Alpha)[0.0667]; ((Epsilon,(Delta,(Gamma,Beta))),Alpha)[0.0667]; ((Gamma,(Delta,(Epsilon,Beta))),Alpha)[0.2000]; ((Gamma,((Epsilon,Delta),Beta)),Alpha)[0.2000]; ((Gamma,(Epsilon,(Delta,Beta))),Alpha)[0.2000]; ((((Epsilon,Delta),Gamma),Beta),Alpha)[0.2000]; (((Epsilon,Delta),(Gamma,Beta)),Alpha)[0.2000]; Output files for usage example 4 File: protpars.fprotpars Protein parsimony algorithm, version 3.69.650 Weights set # 1: 3 trees in all found +--------Gamma ! +--2 +--Epsilon ! ! +--4 ! +--3 +--Delta 1 ! ! +-----Beta ! +-----------Alpha remember: this is an unrooted tree! requires a total of 14.000 +--Epsilon +--4 +--3 +--Delta ! ! +--2 +-----Gamma ! ! 1 +--------Beta ! +-----------Alpha remember: this is an unrooted tree! requires a total of 14.000 [Part of this file has been deleted for brevity] +--Epsilon +-----4 ! +--Delta +--3 ! ! +--Gamma 1 +-----2 ! +--Beta ! +-----------Alpha remember: this is an unrooted tree! requires a total of 2.000 +--------Delta +--3 ! ! +-----Epsilon ! +--4 1 ! +--Gamma ! +--2 ! +--Beta ! +-----------Alpha remember: this is an unrooted tree! requires a total of 2.000 +--------Epsilon +--4 ! ! +-----Delta ! +--3 1 ! +--Gamma ! +--2 ! +--Beta ! +-----------Alpha remember: this is an unrooted tree! requires a total of 2.000 File: protpars.treefile ((Gamma,((Epsilon,Delta),Beta)),Alpha)[0.3333]; ((((Epsilon,Delta),Gamma),Beta),Alpha)[0.3333]; (((Epsilon,Delta),(Gamma,Beta)),Alpha)[0.3333]; ((Gamma,(Delta,(Epsilon,Beta))),Alpha)[0.0667]; (((Epsilon,Gamma),(Delta,Beta)),Alpha)[0.0667]; ((Gamma,((Epsilon,Delta),Beta)),Alpha)[0.0667]; ((Epsilon,(Gamma,(Delta,Beta))),Alpha)[0.0667]; ((Gamma,(Epsilon,(Delta,Beta))),Alpha)[0.0667]; (((Delta,Gamma),(Epsilon,Beta)),Alpha)[0.0667]; (((Delta,(Epsilon,Gamma)),Beta),Alpha)[0.0667]; ((((Epsilon,Delta),Gamma),Beta),Alpha)[0.0667]; ((Epsilon,((Delta,Gamma),Beta)),Alpha)[0.0667]; (((Epsilon,(Delta,Gamma)),Beta),Alpha)[0.0667]; ((Delta,(Gamma,(Epsilon,Beta))),Alpha)[0.0667]; ((Delta,((Epsilon,Gamma),Beta)),Alpha)[0.0667]; (((Epsilon,Delta),(Gamma,Beta)),Alpha)[0.0667]; ((Delta,(Epsilon,(Gamma,Beta))),Alpha)[0.0667]; ((Epsilon,(Delta,(Gamma,Beta))),Alpha)[0.0667]; Data files None Notes None. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 0. Known bugs None. See also Program name Description distmat Create a distance matrix from a multiple sequence alignment ednacomp DNA compatibility algorithm ednadist Nucleic acid sequence distance matrix program ednainvar Nucleic acid sequence invariants method ednaml Phylogenies from nucleic acid maximum likelihood ednamlk Phylogenies from nucleic acid maximum likelihood with clock ednapars DNA parsimony algorithm ednapenny Penny algorithm for DNA eprotdist Protein distance algorithm eprotpars Protein parsimony algorithm erestml Restriction site maximum likelihood method eseqboot Bootstrapped sequences algorithm fdiscboot Bootstrapped discrete sites algorithm fdnacomp DNA compatibility algorithm fdnadist Nucleic acid sequence distance matrix program fdnainvar Nucleic acid sequence invariants method fdnaml Estimate nucleotide phylogeny by maximum likelihood fdnamlk Estimates nucleotide phylogeny by maximum likelihood fdnamove Interactive DNA parsimony fdnapars DNA parsimony algorithm fdnapenny Penny algorithm for DNA fdolmove Interactive Dollo or polymorphism parsimony ffreqboot Bootstrapped genetic frequencies algorithm fproml Protein phylogeny by maximum likelihood fpromlk Protein phylogeny by maximum likelihood fprotdist Protein distance algorithm frestboot Bootstrapped restriction sites algorithm frestdist Calculate distance matrix from restriction sites or fragments frestml Restriction site maximum likelihood method fseqboot Bootstrapped sequences algorithm fseqbootall Bootstrapped sequences algorithm Author(s) This program is an EMBOSS conversion of a program written by Joe Felsenstein as part of his PHYLIP package. Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Written (2004) - Joe Felsenstein, University of Washington. Converted (August 2004) to an EMBASSY program by the EMBOSS team. Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None