eprotpars |
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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 UUU and UUC 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 UUU (Phe) --> CUU (Leu) --> CUA (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 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:
1. Change in different sites is independent. 2. Change in different lineages is independent. 3. 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. 4. 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. 5. 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. 6. 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 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*???? HIPNMGVWABTsince 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!
% eprotpars Protein parsimony algorithm Input (aligned) protein sequence set: protpars.dat Randomize input order of species [N]: Phylip protpars program output file [eprotpars.outfile]: Create a tree file [Y]: Phylip tree output file [eprotpars.treefile]: |
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Protein parsimony algorithm Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers (* if not always prompted): [-sequence] seqset File containing a sequence alignment * -random toggle [N] Randomize input order of species * -randseed integer [3] Random number seed (must be odd) (Any integer value) * -randtimes integer [3] How many times to randomise (Any integer value) * -outgnum integer [1] Number of the outgroup (Integer 1 or more) * -valthresh float [1.0] Threshold value (Number 1.000 or more) [-outfile] outfile [eprotpars.outfile] Phylip protpars program output file [-[no]trout] toggle [Y] Create a tree file * -treefile outfile [eprotpars.treefile] Phylip tree output file Additional (Optional) qualifiers: -[no]besttree toggle [Y] Search for best tree -og toggle [N] Outgroup root -printdata boolean [N] Print out the data at start of run -progress boolean [N] Print indications of progress of run -steps boolean [N] Print out steps in each site -seqatnodes boolean [N] Print sequences at all nodes of tree -[no]drawtree boolean [Y] Draw tree Advanced (Unprompted) qualifiers: -thresh toggle [N] Use Threshold parsimony 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 -odirectory2 string Output directory "-treefile" 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) |
seqset | File containing a sequence alignment | Readable set of sequences | Required |
-random | toggle | Randomize input order of species | Toggle value Yes/No | No |
-randseed | integer | Random number seed (must be odd) | Any integer value | 3 |
-randtimes | integer | How many times to randomise | Any integer value | 3 |
-outgnum | integer | Number of the outgroup | Integer 1 or more | 1 |
-valthresh | float | Threshold value | Number 1.000 or more | 1.0 |
[-outfile] (Parameter 2) |
outfile | Phylip protpars program output file | Output file | eprotpars.outfile |
[-[no]trout] (Parameter 3) |
toggle | Create a tree file | Toggle value Yes/No | Yes |
-treefile | outfile | Phylip tree output file | Output file | eprotpars.treefile |
Additional (Optional) qualifiers | ||||
-[no]besttree | toggle | Search for best tree | Toggle value Yes/No | Yes |
-og | toggle | Outgroup root | Toggle value Yes/No | No |
-printdata | boolean | Print out the data at start of run | Boolean value Yes/No | No |
-progress | boolean | Print indications of progress of run | Boolean value Yes/No | No |
-steps | boolean | Print out steps in each site | Boolean value Yes/No | No |
-seqatnodes | boolean | Print sequences at all nodes of tree | Boolean value Yes/No | No |
-[no]drawtree | boolean | Draw tree | Boolean value Yes/No | Yes |
Advanced (Unprompted) qualifiers | ||||
-thresh | toggle | Use Threshold parsimony | Toggle value Yes/No | No |
Associated qualifiers | ||||
"-sequence" associated seqset 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 |
-scircular1 -scircular_sequence |
boolean | Sequence is circular | Boolean value Yes/No | N |
-squick1 -squick_sequence |
boolean | Read id and sequence only | Boolean value Yes/No | N |
-sformat1 -sformat_sequence |
string | Input sequence format | Any string | |
-iquery1 -iquery_sequence |
string | Input query fields or ID list | Any string | |
-ioffset1 -ioffset_sequence |
integer | Input start position offset | Any integer value | 0 |
-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 | ||||
-odirectory2 -odirectory_outfile |
string | Output directory | Any string | |
"-treefile" 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 AB--EFGHIK Gamma ?BCDSFG*?? Delta CIKDEFGHIK Epsilon DIKDEFGHIK |
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]; |
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 |
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 |
fprotpars | Protein parsimony 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 |
This application was modified for inclusion in EMBOSS by Ian Longden (il@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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