fprotpars 
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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 highrate branch are more probable than one change in a lowrate 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 tencharacter species name that must be blankfilled to be of that length, followed immediately by the species data in the oneletter 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 oneletter 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 sixbase 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.
% 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. 
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Example 2
% fprotpars njumble 3 seed 3 printdata ancseq whichcode m stepbox outgrno 2 thresh 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. 
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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. 
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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. 
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Protein parsimony algorithm Version: EMBOSS:6.4.0.0 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) thresh 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 sformat1 string Input sequence format 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 
Qualifier  Type  Description  Allowed values  Default  

Standard (Mandatory) qualifiers  
[sequence] (Parameter 1) 
seqsetall  File containing one or more sequence alignments  Readable sets of sequences  Required  
[intreefile] (Parameter 2) 
tree  Phylip tree file (optional)  Phylogenetic tree  
[outfile] (Parameter 3) 
outfile  Phylip protpars program output file  Output file  <*>.fprotpars  
Additional (Optional) qualifiers  
weights  properties  Phylip weights file (optional)  Property value(s)  
njumble  integer  Number of times to randomise  Integer 0 or more  0  
seed  integer  Random number seed between 1 and 32767 (must be odd)  Integer from 1 to 32767  1  
outgrno  integer  Species number to use as outgroup  Integer 0 or more  0  
thresh  toggle  Use threshold parsimony  Toggle value Yes/No  No  
threshold  float  Threshold value  Number 1.000 or more  1  
whichcode  list  Use which genetic code 

Universal  
[no]trout  toggle  Write out trees to tree file  Toggle value Yes/No  Yes  
outtreefile  outfile  Phylip tree output file (optional)  Output file  <*>.fprotpars  
printdata  boolean  Print data at start of run  Boolean value Yes/No  No  
[no]progress  boolean  Print indications of progress of run  Boolean value Yes/No  Yes  
[no]treeprint  boolean  Print out tree  Boolean value Yes/No  Yes  
stepbox  boolean  Print steps at each site  Boolean value Yes/No  No  
ancseq  boolean  Print sequences at all nodes of tree  Boolean value Yes/No  No  
[no]dotdiff  boolean  Use dot differencing to display results  Boolean value Yes/No  Yes  
Advanced (Unprompted) qualifiers  
(none)  
Associated qualifiers  
"sequence" associated seqsetall qualifiers  
sbegin1 sbegin_sequence 
integer  Start of each sequence to be used  Any integer value  0  
send1 send_sequence 
integer  End of each sequence to be used  Any integer value  0  
sreverse1 sreverse_sequence 
boolean  Reverse (if DNA)  Boolean value Yes/No  N  
sask1 sask_sequence 
boolean  Ask for begin/end/reverse  Boolean value Yes/No  N  
snucleotide1 snucleotide_sequence 
boolean  Sequence is nucleotide  Boolean value Yes/No  N  
sprotein1 sprotein_sequence 
boolean  Sequence is protein  Boolean value Yes/No  N  
slower1 slower_sequence 
boolean  Make lower case  Boolean value Yes/No  N  
supper1 supper_sequence 
boolean  Make upper case  Boolean value Yes/No  N  
sformat1 sformat_sequence 
string  Input sequence format  Any string  
sdbname1 sdbname_sequence 
string  Database name  Any string  
sid1 sid_sequence 
string  Entryname  Any string  
ufo1 ufo_sequence 
string  UFO features  Any string  
fformat1 fformat_sequence 
string  Features format  Any string  
fopenfile1 fopenfile_sequence 
string  Features file name  Any string  
"outfile" associated outfile qualifiers  
odirectory3 odirectory_outfile 
string  Output directory  Any string  
"outtreefile" associated outfile qualifiers  
odirectory  string  Output directory  Any string  
General qualifiers  
auto  boolean  Turn off prompts  Boolean value Yes/No  N  
stdout  boolean  Write first file to standard output  Boolean value Yes/No  N  
filter  boolean  Read first file from standard input, write first file to standard output  Boolean value Yes/No  N  
options  boolean  Prompt for standard and additional values  Boolean value Yes/No  N  
debug  boolean  Write debug output to program.dbg  Boolean value Yes/No  N  
verbose  boolean  Report some/full command line options  Boolean value Yes/No  Y  
help  boolean  Report command line options and exit. More information on associated and general qualifiers can be found with help verbose  Boolean value Yes/No  N  
warning  boolean  Report warnings  Boolean value Yes/No  Y  
error  boolean  Report errors  Boolean value Yes/No  Y  
fatal  boolean  Report fatal errors  Boolean value Yes/No  Y  
die  boolean  Report dying program messages  Boolean value Yes/No  Y  
version  boolean  Report version number and exit  Boolean value Yes/No  N 
5 10 Alpha ABCDEFGHIK Beta ABEFGHIK Gamma ?BCDSFG*?? Delta CIKDEFGHIK Epsilon DIKDEFGHIK 
5 10 Alpha AABBCCCFHK Beta AABBFHK Gamma ??BBCCCF*? Delta CCIIKKKFHK Epsilon DDIIKKKFHK 5 10 Alpha AADDEGGIIK Beta AAEGGIIK Gamma ??DDSGG??? Delta CCDDEGGIIK Epsilon DDDDEGGIIK 5 10 Alpha AACDDDEGHI Beta AAEGHI Gamma ??CDDDSG*? Delta CCKDDDEGHI Epsilon DDKDDDEGHI 
1111100000 0000011111 
Protein parsimony algorithm, version 3.69 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 
((Gamma,((Epsilon,Delta),Beta)),Alpha)[0.3333]; ((((Epsilon,Delta),Gamma),Beta),Alpha)[0.3333]; (((Epsilon,Delta),(Gamma,Beta)),Alpha)[0.3333]; 
Protein parsimony algorithm, version 3.69 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........ 
(Beta,(Gamma,((Epsilon,Delta),Alpha)))[0.3333]; (Beta,(((Epsilon,Delta),Gamma),Alpha))[0.3333]; (Beta,((Epsilon,Delta),(Gamma,Alpha)))[0.3333]; 
Protein parsimony algorithm, version 3.69 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 
((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]; 
Protein parsimony algorithm, version 3.69 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 
((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]; 
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  Estimates 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  Distance matrix from restriction sites or fragments 
frestml  Restriction site maximum Likelihood method 
fseqboot  Bootstrapped sequences algorithm 
fseqbootall  Bootstrapped sequences algorithm 
Please report all bugs to the EMBOSS bug team (embossbug © emboss.openbio.org) not to the original author.
Converted (August 2004) to an EMBASSY program by the EMBOSS team.