Phylogenetic tree with iTol

Hello everyone!
I am trying to build a phylogenetic tree with iTol. I downloaded all the necessary .qza files and got a very heavy tree of 1243 leaves.
Question: how to reduce the number of leaves and nodes so that everything works more or less quickly.
And how to upload metadata so can see the result of the meta-analysis

Maria

Hello Maria,

In iTOL, you could use the ‘Auto collapse clades’ function to combine / collapse closely related tree tips.

Other software also has function like this. For example, the R package Phyloseq includes the tip_glom() function for collapsing / merging / gloming tree tips.

Let me know if that helps!
Colin

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Hello, Colin! Thank you for your attention!
I filtered my sequences - it turned about 700
And tried to reduce with help "auto collapse’, but
I am not sure, that it done: system wrote: “please provide average branch”
And I deleted branches, but didn’t get faster.

Fortunately, I familiar with R. I try now to do tree with

results<-results %>% mutate(Significant=if_else(we.eBH<0.1,"*", ""))

tree<-drop.tip(tree, tree$tip.label[!tree$tip.label %in% results$Feature.ID]) # remove all the features from the tree we do not have data for
ggtree(tree, layout="circular") %<+% results +
  geom_tippoint(aes(fill=diff.btw), shape=21, color="grey50")  +
  geom_tiplab2(aes(label=Significant), size=10) +
  scale_fill_gradient2(low="darkblue",high="darkred", midpoint = 0, mid="white", name="log2(fold-change") +
  theme(legend.position="right")
ggsave("tree.pdf", height=10, width=10, device="pdf", useDingbats=F)

But what is ```
results<-read_qza(“differentials.qza”)$data

differentials.qza - is problem


Might there is another way to construct tree with R ?

Thank you!
Maria
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So for all of these methods, you have to specify a threshold at which to merge samples. So like on this 1k tip tree, you could list a branch length of 2 and merge tips closer than that.

You will have to select your own threshold!

:1st_place_medal: awesome!

Looks like you are following the qiime2R tutorial. You will have to adjust this to match your own metadata and samples. Like, if you just run

results

has the phyloseq object been imported successfully? Does it have the right number of sequences/ASVs in it?

Colin

1 Like