Revision history [back]

I would like to study the combinatorial class ${\cal H}$ of labelled phylogenetic trees, defined as rooted trees, whose internal nodes are unlabelled and are constrained to have outdegree $\geq 2$, while their leaves have labels attached to them.

According to Flajolet, Sedgewick: Analytic Combinatorics, p. 128, they satisfy the recursive specification $${\cal H}={\cal Z}+\mbox{Set}_{\geq 2}({\cal H})$$ I defined their species $H$ by the code

Z=species.SingletonSpecies()

E2=species.SetSpecies(min=2)

G=CombinatorialSpecies()

H=CombinatorialSpecies()

G.define(E2(Z+G))

G.define(E2.composition(Z+G))

H=Z+G

The number of labelled structures is given by the integer sequence.

In particular I tried to calculate (for a small cardinal number)

1. a list of such structures.
2. a generating series of this structures.
3. the number of such structures.
4. isomorphism-types of such structures.
5. a generating series of the isomorphism-types of such structures.
6. a random such structure.
7. automorphism-groups of of such structures.

using the following code:

1. H.structures([1,2,3]).list().
2. g = H.generating_series().
3. g.counts(3).
4. H.isotypes([1,2,3]).
5. g=H.isotype_generating_series().
6. r=H.structures([1,2,3]).random_element().
7. r.automorphism_group().

Only 2. seems to work.

If my code ist correct, I wonder if some of these (i.e. composition species) are not implemented and when (whether) they will be.

I would like to study the combinatorial class ${\cal H}$ of labelled phylogenetic trees, defined as rooted trees, whose internal nodes are unlabelled and are constrained to have outdegree $\geq 2$, while their leaves have labels attached to them.

According to Flajolet, Sedgewick: Analytic Combinatorics, p. 128, they satisfy the recursive specification $${\cal H}={\cal Z}+\mbox{Set}_{\geq 2}({\cal H})$$ I defined their species $H$ by the code

Z=species.SingletonSpecies()

E2=species.SetSpecies(min=2)

G=CombinatorialSpecies()

H=CombinatorialSpecies()

G.define(E2(Z+G))

G.define(E2.composition(Z+G))

H=Z+G

The number of labelled structures is given by the integer sequence.

In particular I tried to calculate (for a small cardinal number)

1. a list of such structures.
2. a generating series of this structures.
3. the number of such structures.
4. isomorphism-types of such structures.
5. a generating series of the isomorphism-types of such structures.
6. a random such structure.
7. automorphism-groups of of such structures.

using the following code:

1. H.structures([1,2,3]).list().
2. g = H.generating_series().
3. g.counts(3).
4. H.isotypes([1,2,3]).
5. g=H.isotype_generating_series().
6. r=H.structures([1,2,3]).random_element().
7. r.automorphism_group().

Only 2. seems to work.

If my code ist correct, I wonder if some of these (i.e. composition species) are not implemented and when (whether) they will be.

I would like to study the combinatorial class ${\cal H}$ of labelled phylogenetic trees, defined as rooted trees, whose internal nodes are unlabelled and are constrained to have outdegree $\geq 2$, while their leaves have labels attached to them.

According to Flajolet, Sedgewick: Analytic Combinatorics, p. 128, they satisfy the recursive specification $${\cal H}={\cal Z}+\mbox{Set}_{\geq 2}({\cal H})$$ I defined their species $H$ by the code

Z=species.SingletonSpecies()

E2=species.SetSpecies(min=2)

G=CombinatorialSpecies()

H=CombinatorialSpecies()

G.define(E2(Z+G))

H=Z+G

The number of labelled structures is given by the integer sequence.

In particular I tried to calculate (for a small cardinal number)

1. a list of such structures.
2. a generating series of this structures.
3. the number of such structures.
4. isomorphism-types of such structures.
5. a generating series of the isomorphism-types of such structures.
6. a random such structure.
7. automorphism-groups of of such structures.

using the following code:

Only 2. seems to work.

If my code ist correct, I wonder if some of these (i.e. composition species) are not implemented and when (whether) they will be.

I would like to study the combinatorial class ${\cal H}$ of labelled phylogenetic trees, defined as rooted trees, whose internal nodes are unlabelled and are constrained to have outdegree $\geq 2$, while their leaves have labels attached to them.

According to Flajolet, Sedgewick: Analytic Combinatorics, p. 128, they satisfy the recursive specification $${\cal H}={\cal Z}+\mbox{Set}_{\geq 2}({\cal H})$$ I defined their species $H$ by the code

Z=species.SingletonSpecies()

E2=species.SetSpecies(min=2)

G=CombinatorialSpecies()

H=CombinatorialSpecies()

G.define(E2(Z+G))

H=Z+G

The number of labelled structures is given by the integer sequence.

In particular I tried to calculate (for a small cardinal number)

1. a list of such structures.
2. a generating series of this structures.
3. the number of such structures.
4. isomorphism-types of such structures.
5. a generating series of the isomorphism-types of such structures.
6. a random such structure.
7. automorphism-groups of of such structures.

using the following code:

1. H.structures([1,2,3]).list().
H.structures([1,2,3]).list()
2. g = H.generating_series().
H.generating_series()
3. g.counts(3).
g.counts(3)
4. H.isotypes([1,2,3]).
H.isotypes([1,2,3])
5. g=H.isotype_generating_series().
g=H.isotype_generating_series()
6. r=H.structures([1,2,3]).random_element().
r=H.structures([1,2,3]).random_element()
7. r.automorphism_group().
r.automorphism_group()

Only 2. seems to work.

If my code ist correct, I wonder if some of these (i.e. composition species) are not implemented and when (whether) they will be.

I would like to study the combinatorial class ${\cal H}$ of labelled phylogenetic trees, defined as rooted trees, whose internal nodes are unlabelled and are constrained to have outdegree $\geq 2$, while their leaves have labels attached to them.

According to Flajolet, Sedgewick: Analytic Combinatorics, p. 128, they satisfy the recursive specification $${\cal H}={\cal Z}+\mbox{Set}_{\geq 2}({\cal H})$$ I defined their species $H$ by the code

Z=species.SingletonSpecies()

E2=species.SetSpecies(min=2)

G=CombinatorialSpecies()

H=CombinatorialSpecies()

G.define(E2(Z+G))

H=Z+G

The number of labelled structures is given by the integer sequence.

In particular I tried to calculate (for a small cardinal number)

1. a list of such structures.
2. a generating series of this structures.
3. the number of such structures.
4. isomorphism-types of such structures.
5. a generating series of the isomorphism-types of such structures.
6. a random such structure.
7. automorphism-groups of of such structures.

using the following code:

1. H.structures([1,2,3]).list()
2. g = H.generating_series()
3. g.counts(3)
4. H.isotypes([1,2,3])
5. g=H.isotype_generating_series()
6. r=H.structures([1,2,3]).random_element()
7. r.automorphism_group()

Only 2. seems to work.

If my code ist correct, I wonder if some of these (i.e. composition species) are not implemented and when (whether) they will be.

I would like to study the combinatorial class ${\cal H}$ of labelled phylogenetic trees, defined as rooted trees, whose internal nodes are unlabelled and are constrained to have outdegree $\geq 2$, while their leaves have labels attached to them.

According to Flajolet, Sedgewick: Analytic Combinatorics, p. 128, they satisfy the recursive specification $${\cal H}={\cal Z}+\mbox{Set}_{\geq 2}({\cal H})$$ I defined their species $H$ by the code

Z=species.SingletonSpecies()

E2=species.SetSpecies(min=2)

G=CombinatorialSpecies()

H=CombinatorialSpecies()

G.define(E2(Z+G))

H=Z+G

The number of labelled structures is given by the integer sequence.

In particular I tried to calculate (for a small cardinal number)

1. a list of such structures.
2. a generating series of this structures.
3. the number of such structures.
4. isomorphism-types of such structures.
5. a generating series of the isomorphism-types of such structures.
6. a random such structure.
7. automorphism-groups of of such structures.

using the following code:

1. H.structures([1,2,3]).list()
2. g = H.generating_series()
3. g.counts(3)
4. H.isotypes([1,2,3])
5. g=H.isotype_generating_series()
6. r=H.structures([1,2,3]).random_element()
7. r.automorphism_group()

Only 2. seems to work.

If my code ist correct, I wonder if some of these (i.e. composition species) are not implemented and when (whether) they will be.

I would like to study the combinatorial class ${\cal H}$ of labelled phylogenetic trees, defined as rooted trees, whose internal nodes are unlabelled and are constrained to have outdegree $\geq 2$, while their leaves have labels attached to them.

According to Flajolet, Sedgewick: Analytic Combinatorics, p. 128, they satisfy the recursive specification $${\cal H}={\cal Z}+\mbox{Set}_{\geq 2}({\cal H})$$ I defined their species $H$ by the code

Z=species.SingletonSpecies()

E2=species.SetSpecies(min=2)

G=CombinatorialSpecies()

H=CombinatorialSpecies()

G.define(E2(Z+G))

H=Z+G

The number of labelled structures is given by the integer sequence.

In particular I tried to calculate (for a small cardinal number)

1. a list of such structures.
2. a generating series of this structures.
3. the number of such structures.
4. isomorphism-types of such structures.
5. a generating series of the isomorphism-types of such structures.
6. a random such structure.
7. automorphism-groups of of such structures.

using the following code:

1. H.structures([1,2,3]).list()
2. g = H.generating_series()
3. g.counts(3)
4. H.isotypes([1,2,3])
5. g=H.isotype_generating_series()
6. r=H.structures([1,2,3]).random_element()
7. r.automorphism_group()

Only 2. seems to work.

If my code ist correct, I wonder if some of these (i.e. composition species) are not implemented and when (whether) they will be.

I would like to study the combinatorial class ${\cal H}$ of labelled phylogenetic trees, defined as rooted trees, whose internal nodes are unlabelled and are constrained to have outdegree $\geq 2$, while their leaves have labels attached to them.

According to Flajolet, Sedgewick: Analytic Combinatorics, p. 128, they satisfy the recursive specification $${\cal H}={\cal Z}+\mbox{Set}_{\geq 2}({\cal H})$$ I defined their species $H$ by the code

Z=species.SingletonSpecies()

E2=species.SetSpecies(min=2)

G=CombinatorialSpecies()

H=CombinatorialSpecies()

G.define(E2(Z+G))

H=Z+G

The number of labelled structures is given by the integer sequence.

In particular I tried to calculate (for a small cardinal number)

1. a list of such structures.
2. a generating series of this structures.
3. the number of such structures.
4. isomorphism-types of such structures.
5. a generating series of the isomorphism-types of such structures.
6. a random such structure.
7. automorphism-groups of of such structures.

using the following code:

1. H.structures([1,2,3]).list()
2. g = H.generating_series()
3. g.counts(3)
4. H.isotypes([1,2,3])
5. g=H.isotype_generating_series()
6. r=H.structures([1,2,3]).random_element()
7. r.automorphism_group()

Only 2. seems to work.

If my code ist correct, I wonder if some of these (i.e. composition species) are not implemented and when (whether) they will be.

I would like to study the combinatorial class ${\cal H}$ of labelled phylogenetic trees, defined as rooted trees, whose internal nodes are unlabelled and are constrained to have outdegree $\geq 2$, while their leaves have labels attached to them.

According to Flajolet, Sedgewick: Analytic Combinatorics, p. 128, they satisfy this class satisfies the recursive specification $${\cal H}={\cal Z}+\mbox{Set}_{\geq 2}({\cal H})$$ I defined their species $H$ by the code

Z=species.SingletonSpecies()

E2=species.SetSpecies(min=2)

G=CombinatorialSpecies()

H=CombinatorialSpecies()

G.define(E2(Z+G))

H=Z+G

The number of labelled structures is given by the integer sequence.

In particular I tried to calculate (for a small cardinal number)

1. a list of such structures.
2. a generating series of this structures.
3. the number of such structures.
4. isomorphism-types of such structures.
5. a generating series of the isomorphism-types of such structures.
6. a random such structure.
7. automorphism-groups of of such structures.

using the following code:

1. H.structures([1,2,3]).list()
2. g = H.generating_series()
3. g.counts(3)
4. H.isotypes([1,2,3])
5. g=H.isotype_generating_series()
6. r=H.structures([1,2,3]).random_element()
7. r.automorphism_group()

Only 2. seems to work.

If my code ist correct, I wonder if some of these (i.e. composition species) are not implemented and when (whether) they will be.

I would like to study the combinatorial class ${\cal H}$ of labelled phylogenetic trees, defined as rooted trees, whose internal nodes are unlabelled and are constrained to have outdegree $\geq 2$, while their leaves have labels attached to them.

According to Flajolet, Sedgewick: Analytic Combinatorics, p. 128, this class satisfies the recursive specification $${\cal H}={\cal Z}+\mbox{Set}_{\geq 2}({\cal H})$$ I defined their species $H$ by the code

Z=species.SingletonSpecies()

E2=species.SetSpecies(min=2)

G=CombinatorialSpecies()

H=CombinatorialSpecies()

G.define(E2(Z+G))

H=Z+G

The number of labelled structures is given by the integer sequence.

In particular I tried to calculate (for a small cardinal number)

1. a list of such structures.
2. a generating series of this structures.
3. the number of such structures.
4. isomorphism-types of such structures.
5. a generating series of the isomorphism-types of such structures.
6. a random such structure.
7. automorphism-groups of of such structures.

using the following code:

1. H.structures([1,2,3]).list()
2. g = H.generating_series()
3. g.counts(3)
4. H.isotypes([1,2,3])
5. g=H.isotype_generating_series()
6. r=H.structures([1,2,3]).random_element()
7. r.automorphism_group()

Only 2. seems to work.

If my code ist correct, I wonder if some of these (i.e. composition species) are not implemented and when (whether) they will be.

I would like to study the combinatorial class ${\cal H}$ of labelled phylogenetic trees, defined as rooted trees, whose internal nodes are unlabelled and are constrained to have outdegree $\geq 2$, while their leaves have labels attached to them.

According to Flajolet, Sedgewick: Analytic Combinatorics, p. 128, this class satisfies the recursive specification $${\cal H}={\cal Z}+\mbox{Set}_{\geq 2}({\cal H})$$ I defined their species $H$ by the code

Z=species.SingletonSpecies()

E2=species.SetSpecies(min=2)

G=CombinatorialSpecies()

H=CombinatorialSpecies()

G.define(E2(Z+G))

H=Z+G

The number of labelled structures is given by the integer sequence.

In particular I tried to calculate (for a small cardinal number)

1. a list of such structures.
2. a generating series of this structures.
3. the number of such structures.
4. isomorphism-types of such structures.
5. a generating series of the isomorphism-types of such structures.
6. a random such structure.
7. automorphism-groups of of such structures.

using the following code:

1. H.structures([1,2,3]).list()
2. g = H.generating_series()
3. g.counts(3)
4. H.isotypes([1,2,3])
5. g=H.isotype_generating_series()
6. r=H.structures([1,2,3]).random_element()
7. r.automorphism_group()

Only 2. seems to work.

If my code ist correct, I wonder if some of these (i.e. composition species) are not implemented and when (whether) they will be.