ANALYTICS
paleobuddy can now simulate trait-dependent diversification, not just birth-death.
Alternatives · analytics tools
protr alternatives
The best protr alternatives in analytics tools, ranked by Sparkpulse's velocity_score.
Updated Aug 15, 2026
Looking for the best alternatives to protr? Sparkpulse tracks and ranks 12 alternatives in analytics tools by shipping velocity — how frequently each ships meaningful updates, verified from official changelogs. For reference, protr shipped 0 meaningful updates in the last 30 days and carries a velocity score of 0.0 out of 10 in 2026. The alternatives below are ranked the same way, so you're comparing real release momentum, not marketing claims.
About protr
protr's feature set is finished; the work now is surviving Bioconductor's churn.
protr generates numerical descriptors from protein sequences for machine learning, plus alignment-based similarity between sequences. The descriptor functions have been stable for years. Recent releases divide cleanly into two kinds: extending the similarity computations to work under memory constraints, and absorbing the Bioconductor split that moved pairwise alignment out of Biostrings into pwalign.
Velocity 0.0 · Last update 41m ago
Top 12 alternatives to protr
Ranked by recent ship velocity. Tap any card for the full editorial breakdown, or pivot to a head-to-head.
ANALYTICS
geodist stays dependency-free and fast, and warns you when 'cheap' distances stop being honest.
ANALYTICS
errors keeps making uncertainty print the way each scientific field expects.
ANALYTICS
CMAQ went global in v5.5, and has been patching that surface ever since.
ANALYTICS
enpls has not changed its statistics since 2016 — only its website, twice.
ANALYTICS
grex is a lookup table with a version number — it ships when the annotation moves.
ANALYTICS
seriation stopped shipping algorithms and started shipping a way to pick between them.
ANALYTICS
arulesViz finished its move to ggplot2 and has been coasting on maintenance since.
ANALYTICS
EvoPhylo added BEAST2 alongside MrBayes, then went quiet for two years.
ANALYTICS
treespace ships once every year or two, and only when CRAN or a user forces it.
ANALYTICS
Rpath 1.1.0 learns to read Ecopath's own files, easing migration off the desktop tool.
ANALYTICS
TAF keeps turning ICES stock assessments into reproducible, dependency-pinned projects.
protr vs alternatives — shipping velocity at a glance
Velocity score (0–10) and meaningful releases shipped in the last 30 days, from official changelogs. Higher = shipping faster.
| Product | Velocity | Sparks · 30d | Focus areas | Latest release |
|---|---|---|---|---|
| protr (baseline) | 0.0 | 0 | proteomicssequence-descriptorsbioconductor | — |
| paleobuddy | 0.0 | 0 | phylogeneticsdiversificationfossil-record | paleobuddy 1.1.0 adds SSE trait-dependent simulation |
| geodist | 0.0 | 0 | geospatialdistance-calculationzero-dependency | — |
| errors | 0.0 | 0 | uncertainty-propagationmeasurementr-quantities | — |
| CMAQ | 0.0 | 0 | air-qualityatmospheric-modelingepa | CMAQ 5.5 adds global simulation coupled to MPAS-A |
| enpls | 0.0 | 0 | partial-least-squaresensemble-learningchemometrics | — |
| grex | 0.0 | 0 | gtexgene-annotationbioinformatics | — |
| seriation | 0.0 | 0 | seriationmatrix-reorderingoptimization | seriation 1.5.0 adds seriate_best and parallel repeated search |
| arulesViz | 0.0 | 0 | association-rulesvisualizationggplot2 | — |
| EvoPhylo | 0.0 | 0 | phylogeneticsbayesian-inferencebeast2 | — |
| treespace | 0.0 | 0 | phylogeneticstransmission-treescran-compliance | — |
| Rpath | 0.0 | 0 | ecosystem-modelingfisheriesmass-balance | Rpath 1.1.0 imports EwE .eiixml models and estimates P/B |
| TAF | 0.0 | 0 | reproducibilityfisheries-scienceices | TAF 4.0.0 refocuses on ICES and drops every external dependency |
The 12 best protr alternatives, in depth
1. paleobuddy · velocity 0.0
Paleobuddy can now simulate trait-dependent diversification, not just birth-death.
Its velocity score of 0.0/10 reflects longer-term release cadence; its most recent meaningful update was “paleobuddy 1.1.0 adds SSE trait-dependent simulation”.
Where protr leans on proteomics, sequence descriptors and bioconductor, paleobuddy focuses on phylogenetics, diversification and fossil record.
paleobuddy and protr have shipped at a similar pace over the last 30 days, so the decision comes down to fit and feature depth.
Full paleobuddy trajectory → · Compare protr vs paleobuddy →
2. geodist · velocity 0.0
Geodist stays dependency-free and fast, and warns you when 'cheap' distances stop being honest.
Its velocity score of 0.0/10 reflects longer-term release cadence.
Where protr leans on proteomics, sequence descriptors and bioconductor, geodist focuses on geospatial, distance calculation and zero dependency.
geodist and protr have shipped at a similar pace over the last 30 days, so the decision comes down to fit and feature depth.
3. errors · velocity 0.0
Errors keeps making uncertainty print the way each scientific field expects.
Its velocity score of 0.0/10 reflects longer-term release cadence.
Where protr leans on proteomics, sequence descriptors and bioconductor, errors focuses on uncertainty propagation, measurement and r quantities.
errors and protr have shipped at a similar pace over the last 30 days, so the decision comes down to fit and feature depth.
4. CMAQ · velocity 0.0
CMAQ went global in v5.5, and has been patching that surface ever since.
Its velocity score of 0.0/10 reflects longer-term release cadence; its most recent meaningful update was “CMAQ 5.5 adds global simulation coupled to MPAS-A”.
Where protr leans on proteomics, sequence descriptors and bioconductor, CMAQ focuses on air quality, atmospheric modeling and epa.
CMAQ and protr have shipped at a similar pace over the last 30 days, so the decision comes down to fit and feature depth.
5. enpls · velocity 0.0
Enpls has not changed its statistics since 2016 — only its website, twice.
Its velocity score of 0.0/10 reflects longer-term release cadence.
Where protr leans on proteomics, sequence descriptors and bioconductor, enpls focuses on partial least squares, ensemble learning and chemometrics.
enpls and protr have shipped at a similar pace over the last 30 days, so the decision comes down to fit and feature depth.
6. grex · velocity 0.0
Grex is a lookup table with a version number — it ships when the annotation moves.
Its velocity score of 0.0/10 reflects longer-term release cadence.
Where protr leans on proteomics, sequence descriptors and bioconductor, grex focuses on gtex, gene annotation and bioinformatics.
grex and protr have shipped at a similar pace over the last 30 days, so the decision comes down to fit and feature depth.
7. seriation · velocity 0.0
Seriation stopped shipping algorithms and started shipping a way to pick between them.
Its velocity score of 0.0/10 reflects longer-term release cadence; its most recent meaningful update was “seriation 1.5.0 adds seriate_best and parallel repeated search”.
Where protr leans on proteomics, sequence descriptors and bioconductor, seriation focuses on seriation, matrix reordering and optimization.
seriation and protr have shipped at a similar pace over the last 30 days, so the decision comes down to fit and feature depth.
8. arulesViz · velocity 0.0
ArulesViz finished its move to ggplot2 and has been coasting on maintenance since.
Its velocity score of 0.0/10 reflects longer-term release cadence.
Where protr leans on proteomics, sequence descriptors and bioconductor, arulesViz focuses on association rules, visualization and ggplot2.
arulesViz and protr have shipped at a similar pace over the last 30 days, so the decision comes down to fit and feature depth.
9. EvoPhylo · velocity 0.0
EvoPhylo added BEAST2 alongside MrBayes, then went quiet for two years.
Its velocity score of 0.0/10 reflects longer-term release cadence.
Where protr leans on proteomics, sequence descriptors and bioconductor, EvoPhylo focuses on phylogenetics, bayesian inference and beast2.
EvoPhylo and protr have shipped at a similar pace over the last 30 days, so the decision comes down to fit and feature depth.
10. treespace · velocity 0.0
Treespace ships once every year or two, and only when CRAN or a user forces it.
Its velocity score of 0.0/10 reflects longer-term release cadence.
Where protr leans on proteomics, sequence descriptors and bioconductor, treespace focuses on phylogenetics, transmission trees and cran compliance.
treespace and protr have shipped at a similar pace over the last 30 days, so the decision comes down to fit and feature depth.
11. Rpath · velocity 0.0
Rpath 1.1.0 learns to read Ecopath's own files, easing migration off the desktop tool.
Its velocity score of 0.0/10 reflects longer-term release cadence; its most recent meaningful update was “Rpath 1.1.0 imports EwE .eiixml models and estimates P/B”.
Where protr leans on proteomics, sequence descriptors and bioconductor, Rpath focuses on ecosystem modeling, fisheries and mass balance.
Rpath and protr have shipped at a similar pace over the last 30 days, so the decision comes down to fit and feature depth.
12. TAF · velocity 0.0
TAF keeps turning ICES stock assessments into reproducible, dependency-pinned projects.
Its velocity score of 0.0/10 reflects longer-term release cadence; its most recent meaningful update was “TAF 4.0.0 refocuses on ICES and drops every external dependency”.
Where protr leans on proteomics, sequence descriptors and bioconductor, TAF focuses on reproducibility, fisheries science and ices.
TAF and protr have shipped at a similar pace over the last 30 days, so the decision comes down to fit and feature depth.
Frequently asked questions
What are the best alternatives to protr?
The top protr alternatives we currently track in analytics tools are paleobuddy, geodist, errors, CMAQ, enpls, ranked by recent ship velocity.
How is this list of protr alternatives ranked?
Alternatives are ranked by Sparkpulse's velocity_score — release cadence + 30-day spark count + sector-relative ship rate.
Can I compare protr directly with one of these alternatives?
Yes — every card has a "Compare with protr" link to a side-by-side /compare page.