Get branch support values for phylogenetic tree
I have been working with Nucleotide/Amino acids data (multiple sequence alignment files) to generate maximum parsimony tree.
To evaluate the tree topology I then used bootstrap and then I have used a function (get_support) from biopython 1.73 package, in order to get the branch support for the tree I had generated, which is as follows:
def get_support(target_tree, trees, len_trees=None):
"""Calculate branch support for a target tree given bootstrap replicate trees.
:Parameters:
target_tree : Tree
tree to calculate branch support for.
trees : iterable
iterable of trees used to calculate branch support.
len_trees : int
optional count of replicates in trees. len_trees must be provided
when len(trees) is not a valid operation.
"""
term_names = sorted(term.name
for term in target_tree.find_clades(terminal=True))
bitstrs = {}
size = len_trees
if size is None:
try:
size = len(trees)
except TypeError:
raise TypeError("Trees does not support len(trees), "
"you must provide the number of replicates in trees "
"as the optional parameter len_trees.")
for clade in target_tree.find_clades(terminal=False):
bitstr = _clade_to_bitstr(clade, term_names)
bitstrs[bitstr] = (clade, 0)
for tree in trees:
for clade in tree.find_clades(terminal=False):
bitstr = _clade_to_bitstr(clade, term_names)
if bitstr in bitstrs:
c, t = bitstrs[bitstr]
c.confidence = (t + 1) * 100.0 / size
round (c.confidence)
bitstrs[bitstr] = (c, t + 1)
return target_tree
When I use this method to get the branch support for my tree, it draws a tree with branch support values for few of the branches and not for all of them.
support_tree = get_support(pars_tree, tree)
Phylo.draw(support_tree)
get_support() is function which accepts the tree for which branch support is calculated and tree is the list of replicate trees generated under bootstrap function. Does anyone have idea for what could possibly be the reason for it?
I am stuck at this point , can anyone have suggestions for this?
python
asked 15 mins ago
Sidra Younas
1011
New contributor
Sidra Younas is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
add a comment |
I have been working with Nucleotide/Amino acids data (multiple sequence alignment files) to generate maximum parsimony tree.
To evaluate the tree topology I then used bootstrap and then I have used a function (get_support) from biopython 1.73 package, in order to get the branch support for the tree I had generated, which is as follows:
def get_support(target_tree, trees, len_trees=None):
"""Calculate branch support for a target tree given bootstrap replicate trees.
:Parameters:
target_tree : Tree
tree to calculate branch support for.
trees : iterable
iterable of trees used to calculate branch support.
len_trees : int
optional count of replicates in trees. len_trees must be provided
when len(trees) is not a valid operation.
"""
term_names = sorted(term.name
for term in target_tree.find_clades(terminal=True))
bitstrs = {}
size = len_trees
if size is None:
try:
size = len(trees)
except TypeError:
raise TypeError("Trees does not support len(trees), "
"you must provide the number of replicates in trees "
"as the optional parameter len_trees.")
for clade in target_tree.find_clades(terminal=False):
bitstr = _clade_to_bitstr(clade, term_names)
bitstrs[bitstr] = (clade, 0)
for tree in trees:
for clade in tree.find_clades(terminal=False):
bitstr = _clade_to_bitstr(clade, term_names)
if bitstr in bitstrs:
c, t = bitstrs[bitstr]
c.confidence = (t + 1) * 100.0 / size
round (c.confidence)
bitstrs[bitstr] = (c, t + 1)
return target_tree
When I use this method to get the branch support for my tree, it draws a tree with branch support values for few of the branches and not for all of them.
support_tree = get_support(pars_tree, tree)
Phylo.draw(support_tree)
get_support() is function which accepts the tree for which branch support is calculated and tree is the list of replicate trees generated under bootstrap function. Does anyone have idea for what could possibly be the reason for it?
I am stuck at this point , can anyone have suggestions for this?
python
asked 15 mins ago
Sidra Younas
1011
New contributor
Sidra Younas is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
add a comment |
I have been working with Nucleotide/Amino acids data (multiple sequence alignment files) to generate maximum parsimony tree.
To evaluate the tree topology I then used bootstrap and then I have used a function (get_support) from biopython 1.73 package, in order to get the branch support for the tree I had generated, which is as follows:
def get_support(target_tree, trees, len_trees=None):
"""Calculate branch support for a target tree given bootstrap replicate trees.
:Parameters:
target_tree : Tree
tree to calculate branch support for.
trees : iterable
iterable of trees used to calculate branch support.
len_trees : int
optional count of replicates in trees. len_trees must be provided
when len(trees) is not a valid operation.
"""
term_names = sorted(term.name
for term in target_tree.find_clades(terminal=True))
bitstrs = {}
size = len_trees
if size is None:
try:
size = len(trees)
except TypeError:
raise TypeError("Trees does not support len(trees), "
"you must provide the number of replicates in trees "
"as the optional parameter len_trees.")
for clade in target_tree.find_clades(terminal=False):
bitstr = _clade_to_bitstr(clade, term_names)
bitstrs[bitstr] = (clade, 0)
for tree in trees:
for clade in tree.find_clades(terminal=False):
bitstr = _clade_to_bitstr(clade, term_names)
if bitstr in bitstrs:
c, t = bitstrs[bitstr]
c.confidence = (t + 1) * 100.0 / size
round (c.confidence)
bitstrs[bitstr] = (c, t + 1)
return target_tree
When I use this method to get the branch support for my tree, it draws a tree with branch support values for few of the branches and not for all of them.
support_tree = get_support(pars_tree, tree)
Phylo.draw(support_tree)
get_support() is function which accepts the tree for which branch support is calculated and tree is the list of replicate trees generated under bootstrap function. Does anyone have idea for what could possibly be the reason for it?
I am stuck at this point , can anyone have suggestions for this?
python
asked 15 mins ago
Sidra Younas
1011
New contributor
Sidra Younas is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
I have been working with Nucleotide/Amino acids data (multiple sequence alignment files) to generate maximum parsimony tree.
To evaluate the tree topology I then used bootstrap and then I have used a function (get_support) from biopython 1.73 package, in order to get the branch support for the tree I had generated, which is as follows:
def get_support(target_tree, trees, len_trees=None):
"""Calculate branch support for a target tree given bootstrap replicate trees.
:Parameters:
target_tree : Tree
tree to calculate branch support for.
trees : iterable
iterable of trees used to calculate branch support.
len_trees : int
optional count of replicates in trees. len_trees must be provided
when len(trees) is not a valid operation.
"""
term_names = sorted(term.name
for term in target_tree.find_clades(terminal=True))
bitstrs = {}
size = len_trees
if size is None:
try:
size = len(trees)
except TypeError:
raise TypeError("Trees does not support len(trees), "
"you must provide the number of replicates in trees "
"as the optional parameter len_trees.")
for clade in target_tree.find_clades(terminal=False):
bitstr = _clade_to_bitstr(clade, term_names)
bitstrs[bitstr] = (clade, 0)
for tree in trees:
for clade in tree.find_clades(terminal=False):
bitstr = _clade_to_bitstr(clade, term_names)
if bitstr in bitstrs:
c, t = bitstrs[bitstr]
c.confidence = (t + 1) * 100.0 / size
round (c.confidence)
bitstrs[bitstr] = (c, t + 1)
return target_tree
When I use this method to get the branch support for my tree, it draws a tree with branch support values for few of the branches and not for all of them.
support_tree = get_support(pars_tree, tree)
Phylo.draw(support_tree)
get_support() is function which accepts the tree for which branch support is calculated and tree is the list of replicate trees generated under bootstrap function. Does anyone have idea for what could possibly be the reason for it?
I am stuck at this point , can anyone have suggestions for this?
python
python
asked 15 mins ago
Sidra Younas
1011
New contributor
Sidra Younas is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked 15 mins ago
Sidra Younas
1011
New contributor
Sidra Younas is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked 15 mins ago
Sidra Younas
1011
New contributor
Sidra Younas is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked 15 mins ago
Sidra Younas
1011
asked 15 mins ago
Sidra Younas
1011
1011
New contributor
Sidra Younas is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
New contributor
Sidra Younas is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
Sidra Younas is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
add a comment |
add a comment |
active
oldest
votes
Your Answer
StackExchange.ifUsing("editor", function () {
return StackExchange.using("mathjaxEditing", function () {
StackExchange.MarkdownEditor.creationCallbacks.add(function (editor, postfix) {
StackExchange.mathjaxEditing.prepareWmdForMathJax(editor, postfix, [["\$", "\$"]]);
});
});
}, "mathjax-editing");
StackExchange.ifUsing("editor", function () {
StackExchange.using("externalEditor", function () {
StackExchange.using("snippets", function () {
StackExchange.snippets.init();
});
});
}, "code-snippets");
StackExchange.ready(function() {
var channelOptions = {
tags: "".split(" "),
id: "196"
};
initTagRenderer("".split(" "), "".split(" "), channelOptions);
StackExchange.using("externalEditor", function() {
// Have to fire editor after snippets, if snippets enabled
if (StackExchange.settings.snippets.snippetsEnabled) {
StackExchange.using("snippets", function() {
createEditor();
});
}
else {
createEditor();
}
});
function createEditor() {
StackExchange.prepareEditor({
heartbeatType: 'answer',
autoActivateHeartbeat: false,
convertImagesToLinks: false,
noModals: true,
showLowRepImageUploadWarning: true,
reputationToPostImages: null,
bindNavPrevention: true,
postfix: "",
imageUploader: {
brandingHtml: "Powered by u003ca class="icon-imgur-white" href="https://imgur.com/"u003eu003c/au003e",
contentPolicyHtml: "User contributions licensed under u003ca href="https://creativecommons.org/licenses/by-sa/3.0/"u003ecc by-sa 3.0 with attribution requiredu003c/au003e u003ca href="https://stackoverflow.com/legal/content-policy"u003e(content policy)u003c/au003e",
allowUrls: true
},
onDemand: true,
discardSelector: ".discard-answer"
,immediatelyShowMarkdownHelp:true
});
}
});
Sidra Younas is a new contributor. Be nice, and check out our Code of Conduct.
Sign up or log in
StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Post as a guest
Required, but never shown
StackExchange.ready(
function () {
StackExchange.openid.initPostLogin('.new-post-login', 'https%3a%2f%2fcodereview.stackexchange.com%2fquestions%2f210680%2fget-branch-support-values-for-phylogenetic-tree%23new-answer', 'question_page');
}
);
Post as a guest
Required, but never shown
active
oldest
votes
active
oldest
votes
active
oldest
votes
active
oldest
votes
Sidra Younas is a new contributor. Be nice, and check out our Code of Conduct.
Sidra Younas is a new contributor. Be nice, and check out our Code of Conduct.
Sidra Younas is a new contributor. Be nice, and check out our Code of Conduct.
Sidra Younas is a new contributor. Be nice, and check out our Code of Conduct.
Thanks for contributing an answer to Code Review Stack Exchange!
- Please be sure to answer the question. Provide details and share your research!
But avoid …
- Asking for help, clarification, or responding to other answers.
- Making statements based on opinion; back them up with references or personal experience.
Use MathJax to format equations. MathJax reference.
To learn more, see our tips on writing great answers.
Some of your past answers have not been well-received, and you're in danger of being blocked from answering.
Please pay close attention to the following guidance:
- Please be sure to answer the question. Provide details and share your research!
But avoid …
- Asking for help, clarification, or responding to other answers.
- Making statements based on opinion; back them up with references or personal experience.
To learn more, see our tips on writing great answers.
Sign up or log in
StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Post as a guest
Required, but never shown
StackExchange.ready(
function () {
StackExchange.openid.initPostLogin('.new-post-login', 'https%3a%2f%2fcodereview.stackexchange.com%2fquestions%2f210680%2fget-branch-support-values-for-phylogenetic-tree%23new-answer', 'question_page');
}
);
Post as a guest
Required, but never shown
Sign up or log in
StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Post as a guest
Required, but never shown
Sign up or log in
StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Post as a guest
Required, but never shown
Sign up or log in
StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Post as a guest
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
