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All options

> Input parameters
> Basic costs
> Options
> Reconciliation graph parameters
> Amalgamation parameters
> Pareto-optimality parameters


Species file : please enter either :
  1. Select a file:
  2. or paste your data here:


Gene file : please enter either :
  1. Select a file:
  2. or paste your data here:


Parameter file (optionnal) : please enter either :
  1. Select a file:
  2. or paste your data here:





Collapse mode ?
Dated ?

Gene mapping file (optionnal) : please enter either :
  1. Select a file:
  2. or paste your data here:

Print newick ?
Resolve trees ?
Transfer dead ?


Print graph ?
Print reconciliations ?


Amalgamate ?
Fix dtl costs ?


Pareto-optimality algorithm to use
Real epsilon ?


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Some explanations about the options


Reconciliation graph parameters

Print graph
Print the graph representation of all possible MPRs to the file given by print.graph.file, with a number identifying the gene tree, if there are multiple gene trees. If keep.only.canonical.reconciliations is true, the canonical graph [1] will be printed with the suffix “_canonical.sif”, with a prefix if given by output.prefix to the directory specified by output.dir. These graphs can be visualized with Cytoscape (http://www.cytoscape.org/).
Print reconciliation info
Print reconciliation information.
Print reconciliations
Print the median reconciliations and a random reconciliation if the value is 1 and all reconciliations if the value is 2, up to the limit given by solution.limit. If check.time.consistency=1, then only consistent reconciliations will be printed for a value of 2.
Keep only canonical reconciliations
If true, the program simplifies the graph of all possible reconciliations by removing non-canonical reconciliations. Only canonical reconciliations will be printed.
Sylvx reconciliation
Print the reconciliations using the Sylvx format (http://www.sylvx.org). Additionally, an accompanying species tree with the suffix “_sylvx_species.txt” will be printed.
Solution limit
The maximum of reconciliations to print if print.reconciliations=All reconciliations.

Pareto-optimality parameters

Min reconciliations
The reconciliation calculation is repeated with increasing values of epsilon until the number of reconciliations in the solution space is greater than min.recs.
Min reconciliations increment
To be used in combination with the min.recs parameter; it sets the increments of epsilon.
Max epsilon value
To be used in combination with the min.recs parameter; it sets the maximum epsilon value to try.
nD
valid values are between 0 and 1, inclusive. Optional parameters for pareto.mod 1. It is the percentage of the ratio r=duplication cost/transfer cost that defines the interval for this ratio cost, which is [r-nD*r;r+nD*r]. This is taken as input of strategy s3
nDL
valid values are between 0 and 1, inclusive Similar to nD, but for the ratio duplication cost/loss cost.
nL
valid values are between 0 and 1, inclusive Similar to nD, but for the ratio loss cost/transfer cost.
Pareto-optimality algorithm to use
Pareto-optimality algorithm to use (see above). 1 corresponds to “strategy s3” in [5], 2 corresponds to “strategy s4” in [5], and 3 corresponds to “strategy s5” in [5]. The Pareto-optimal algorithm is not used if pareto.mod=0.
Real epsilon
The epsilon value given by suboptimal.epsilon will be considered a real value rather than a percentage.
Suboptimal epsilon
Additional parameter for pareto.mod=1,2,3. If greater than 0, then non-optimal reconciliations will be included in the graph [5] if their cost is within suboptimal.epsilon% of the optimal. For example, if suboptimal=2 and the optimal cost found is 36, then not only will all reconciliations with a cost of 36 will be generated, but also any Pareto-optimal reconciliations with a cost less than or equal to 36.72, i.e. those within 2% of the optimal. If this parameter is omitted, or the given value is negative, then no constraint on the over-cost is imposed, i.e. suboptimal.epsilon=+infinity.

Input parameters

Species file
The path to the species file in Newick format. The tree must be binary. The tree can either be undated, fully dated or partially dated. If the tree is fully dated, there are two ways to specify its dates: either the species tree has branch lengths and is ultrametric (note that branch lengths are given after the a colon; see the tree in tests/Stree.tree for an example), in which case an ordering of species nodes will be deduced from the branch lengths, or an ordering of species nodes can be given directly in the bootstrap fields (dates.as.bootstrap=true, see the tree in tests/StreeBS.tree for an example). In case the tree is partially dated, only the latter option is possible.
Gene file
The path to a gene file in Newick format. This file can contain more than one gene tree. A reconciliation with the species tree will be performed on each gene tree, unless the gene trees are amalgamated (amalgate=true). If a gene tree is unrooted, it will either be rooted randomly or with an optimal rooting if resolve.trees=true [manuscript in preparation]. Similarly non-binary gene trees will be binary by choosing a random resolution per each polytomy unless resolve.trees=true, in which case all possible binary resolutions will be considered in an efficient manner [manuscript in preparation].
Character used as separator for gene names in the gene trees.
The character used as separator for gene names in the gene trees. For example, if 'char.sep=_' is given as an option, then the gene HOMO_2 corresponds to the taxa HOMO.
Parameter file (optionnal)
If a valid file is given, parameters will also be read from the file in the same format NAME=VALUE. Any parameters given on the command line will take precedence and the dupilcated parameter will be ignored.
Select the name of a file or the actual data
if you are using Netscape 2.x or later, you can select a file by typing its name, or better, by selecting it with the Netscape file browser (Browse button)
OR you can type your data in the next area, or cut and paste it from another application.
(but not both)

Options

Collapse mode
If given a value of 0 or 1, gene tree nodes whose values are strictly below collapse.threshold are merged to create polytomies. The values are either the distances to the father node (collapse.mode=0) or bootstrap values (collapse.mode=1).
Collapse threshold
Threshold used to collapse gene tree nodes if collapse.mode is 0 or 1.
Consider transfers as a possible event
Consider transfers as a possible event. If false, transfers and transfer loss are not considered.
Consider transfer loss as a possible event
Consider transfer loss as a possible event.
Dated
If 0, the species tree is considered to be undated. If 1, the species tree is considered to be partially dated. Note that the dates must be given as bootstrap values (thus dates.as.bootstrap is automatically set to true). If 2 (default), the species tree is considered to be fully dated and thus it either has branch lengths and is ultrametric (and in this case an ordering of species nodes is deduced from the branch lengths) or fully ordered (and in this case dates.as.bootstrap has to be set as true).
Date as bootstrap
If true, the species node ordering is read directly from the bootstrap values (see the tree in tests/StreeBS.tree for an example), the root having the highest value. Leaves are considered to have a value of 0.
Check time consistency
Check whether the returned reconciliations are time consistent (undated and partially dated species trees only).
Check time consistency all
Check the time consistency of all reconciliations up to the limit consistency.limit (undated and partially dated species trees only).
Consistency limit
The maximum number of reconciliations to check if check.time.consistency.all=true (undated and partially dated species trees only).
Gene mapping file (optionnal)
A file with mapping between gene names and species names using a space as a separator (i.e., each line is gene_name species_name). Otherwise, gene names must be start with a valid species name followed by the separator char.sep.
Orthology output
Print all pairs of orthologous genes.
Print newick
The species tree and the binary, rooted gene tree used in the calculation of the MPR are printed in Newick format to the file print.newick.species.tree.file and print.newick.gene.tree.file respectively. If the given gene trees are amalgamated, or the given gene tree is unrooted/non-binary, the resulting (optimal) rooted binary gene tree is printed. The internal node ids corresponding to the printed reconciliations are printed as bootstrap values. A number identifying the gene tree will be appended to the file name if there are multiple gene trees.
Resolve trees
If true, the algorithm will consider all possible resolutions of non-binary nodes (polytomies) and all possible rootings of unrooted gene trees in an efficient way [manuscript in preparation].
Transfer dead
If true, horizontal gene transfers are allowed with species other than those in the specie tree (thus extinct or unsampled species)
Trim species tree
If true, unneeded nodes of the species tree (i.e. nodes that will never be considered in an optimal reconciliation) will be removed before calculating the matrix. Trimming the species tree can improve the performance of the matrix calculation.
Ultrametric only
Return an error if the dated species tree is not ultrametric.

Basic costs

The cost of a gene duplication
The cost of a gene duplication
The cost of a gene transfer (HGT)
The cost of a horizontal gene transfer (HGT)
The cost of a gene loss
The cost of a gene loss

Amalgamation parameters

The gene input file is in the ALE format
The gene input file is in the ALE format (thus amalgamate is automatically set to true)
Amalgamate
If true, an amalgamation of the gene trees is used to compute the reconciliation.
Weight amalgamation
The weight by which the clade supports are multiplied in the amalgamation.
Max iterations
If greater than one, the costs and amalgamation weight will be updated at most max.iterations times, until the costs and amalgamation weight converge (to know how the costs and the amalgamation weight are updated)
Fix dtl costs
If true, when costs are updated while iterating (see max.iterations), only the amalgamation weight will be updated

References:
http://mbb.univ-montp2.fr/MBB/subsection/softExec.php?soft=eccetera

Based on Pise form generator version: 5.a (08 mars 2017 14:19)