Simply use the iterations option (e.g. -n 1000) of IQTREE. It's a lot quicker (several logs) and is strongly of identical performance to RAxML.

iqtree -s alignment.phy -n 1000 -m GTR+I+G -nt 4

It takes phylip, fasta, nexus ... and no-one questions 1000 iterations, so you're safe.

I personally I'd then go on to bootstrap the tree (IQTREE is extremely fast). If you were bootstrapping with iterations RAxML is unworkable, you'd need e.g. 10 iterations per bootstrap (1000 bootstraps) and would be time consuming. IQTREE could easily perform 10 iterations per bootstrap and would accommodate 100 iterations (1000 would be a bit excessive for bootstrapping).

RAxML is old program now, IQTREE is its successfully and massively refactored maximum likelihood phylogeny.

If you don't understand the command line, drop a note and I'll explain the model it's using.

Simply use the iterations option (e.g. -n 1000) of IQTREE. It's a lot quicker (several logs) and is strongly of identical performance to RAxML.

iqtree -s alignment.phy -n 1000 -m GTR+I+G -nt 4

It takes phylip, fasta, nexus ... and no-one questions 1000 iterations, so you're safe.

I personally I'd then go on to bootstrap the tree (IQTREE is extremely fast). If you were bootstrapping with iterations RAxML is unworkable, you'd need e.g. 10 iterations per bootstrap (1000 bootstraps) and would be time consuming. IQTREE could easily perform 10 iterations per bootstrap and would accommodate 100 iterations (1000 would be a bit excessive for bootstrapping).

RAxML is an old program now, IQTREE is its successor and massively refactored for maximum likelihood phylogeny.

If you don't understand the command line, drop a note and I'll explain the model it's using.

Simply use the iterations option (e.g. -n 1000) of IQTREE. It's a lot quicker and is strongly of identical performance to RAxML.

iqtree -s alignment.phy -n 1000 -m GTR+I+G -nt 4

It takes phylip, fasta, nexus ... no one questions 1000 iterations.

I personally then go on an bootstrap the tree.

If you don't understand the command line, drop a note and I'll explain the model its using.

Simply use the iterations option (e.g. -n 1000) of IQTREE. It's a lot quicker (several logs) and is strongly of identical performance to RAxML.

iqtree -s alignment.phy -n 1000 -m GTR+I+G -nt 4

It takes phylip, fasta, nexus ... and no-one questions 1000 iterations, so you're safe.

I personally I'd then go on to bootstrap the tree (IQTREE is extremely fast). If you were bootstrapping with iterations RAxML is unworkable, you'd need e.g. 10 iterations per bootstrap (1000 bootstraps) and would be time consuming. IQTREE could easily perform 10 iterations per bootstrap and would accommodate 100 iterations (1000 would be a bit excessive for bootstrapping).

RAxML is old program now, IQTREE is its successfully and massively refactored maximum likelihood phylogeny.

If you don't understand the command line, drop a note and I'll explain the model it's using.