EnvNJ
Whole Genome Phylogenies Using Sequence Environments
Description
Contains utilities for the analysis of protein sequences in a phylogenetic context. Allows the generation of phylogenetic trees base on protein sequences in an alignment-independent way. Two different methods have been implemented. One approach is based on the frequency analysis of n-grams, previously described in Stuart et al. (2002) <doi:10.1093/bioinformatics/18.1.100>. The other approach is based on the species-specific neighborhood preference around amino acids. Features include the conversion of a protein set into a vector reflecting these neighborhood preferences, pairwise distances (dissimilarity) between these vectors, and the generation of trees based on these distance matrices.
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CRAN Check Status
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | NOTE |
| r-devel-linux-x86_64-debian-gcc | NOTE |
| r-devel-linux-x86_64-fedora-clang | NOTE |
| r-devel-linux-x86_64-fedora-gcc | NOTE |
| r-devel-windows-x86_64 | NOTE |
| r-oldrel-macos-arm64 | NOTE |
| r-oldrel-macos-x86_64 | NOTE |
| r-oldrel-windows-x86_64 | NOTE |
| r-patched-linux-x86_64 | NOTE |
| r-release-linux-x86_64 | NOTE |
| r-release-macos-arm64 | NOTE |
| r-release-macos-x86_64 | NOTE |
| r-release-windows-x86_64 | NOTE |
Check details (13 non-OK)
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
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Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Check History
NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Rd files
checkRd: (-1) metrics.Rd:124: Lost braces
124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
| ^
Code
Code metrics have not been computed for this package yet.