Clustal omega, for example.

A very simple and ultra rapid application works from the Unix/Linux command line with the program Clustal installed. With all your sequences to be aligned in a simple fasta file named "test" you type just one command: clustalw test;clustalw -outputtree=dist -tree -infile=test.aln;l test.aln;l test.dst. This command gives you the following output files:

1, multiple alignment

2, distance matrix

3, a description of a simple phylogenetic (neighbor-joining) tree (test.ph). The latter can be imported or even simply pasted in a program such as FigTree for visualisation

Dear Japheth E. Gado

as Abhijeet Singh alredy wrote, CLustal Omega

https://www.ebi.ac.uk/Tools/msa/clustalo/

can provide you as the identity matrix as output, This matrix could be easly imported in excel of other software.

An example of this is avaialble at the minute 2 of the following video

https://www.youtube.com/watch?v=pujCNbwpUtE

extracted from my blog, ProteoCool

best regards

Manuele

The R package bio3d: http://thegrantlab.org/bio3d/index.html

has the function seqidentity: http://thegrantlab.org/bio3d/reference/seqidentity.html

and approach to plot the PID heatmap with ggplot2 would be:

#calculate PID

mat %

gather(seq2, pid, - 1) %>%

mutate(seq = fct_inorder(seq),

seq2 = fct_inorder(seq2),

pid2 = ifelse(!is.na(pid), paste0(pid * 100, "%"), NA_character_)) %>%

ggplot()+

geom_tile(aes(x = seq, y = seq2, fill = pid)) +

scale_fill_gradient(low = "white",

high = "13ae4b",

na.value = "white",

breaks = c(0, 0.2, 0.4, 0.6, 0.8, 1),

limits = c(0, 1)) +

geom_text(aes(x = seq, y = seq2, label = pid2)) +

theme_classic() +

scale_x_discrete(position = "top") +

theme(legend.position = "none") +

xlab("") +

ylab("") +

coord_equal()